Publications

Cobbin, D & Choi, V 2014, Tracking Down the Hand Yangming Channel Locations and Functions of Acupoints of the Large Intestine Channel, GHR Studio.
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Although drawn from the study of the Large Intestine Channel these are equally relevant to all channels and fundamental CM theory. This is a valuable practical and clinically applicable resource for students and practitioners alike.

Hoppenrath, M, Murray, SA, Chomérat, N & Horiguchi, T 2014, Marine benthic dinoflagellates - unveiling their worldwide biodiversity, 1, Senckenberg, Stuttgart.
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This publication presents the first summary of our knowledge of benthic dinoflagellate species. Dinoflagellates are important primary producers and symbionts, but, at the same time, also consumers and parasites. Species compositions of benthic habitats are quite distinct from those of planktonic habitats. Less than 10% of the approximately 2000 described extant dinoflagellate species appear to be benthic. They occur in different types of habitats (chapter II) and their morphology, their behavior, and some of their life cycles (chapter VI) seem to be well adapted to the benthic lifestyle. Information on their geographic distribution is still very limited and is compiled herein (chapter V). The study of harmful benthic dinoflagellates started in the late 1970s when it was suspected that a benthic species, later named Gambierdiscus toxicus, was responsible for ciguatera fish poisoning, a type of human poisoning linked to the consumption of certain species of tropical reef fish. As the number of ciguatera fish poisoning incidents increases, and the distribution of toxin producing benthic taxa seems to be expanding, detailed understanding of the species diversity and the ability to accurately identify them is becoming increasingly important (chapter VII). Dinoflagellate classification is currently undergoing changes and far from being settled, as new species and genera are discovered and systematic entities are rearranged. Many benthic dinoflagellate genera have unusual morphologies and appear to be only remotely related to known planktonic taxa, so that molecular phylogenetic analyses frequently show little statistical support for any relationship (chapter IV). Benthic species display unique thecal plate arrangements compared to planktonic species, e.g. Adenoides, Amphidiniella, Cabra, Planodinium, Sabulodinium, Rhinodinium (chapter III). Therefore, no classification on higher rank levels (e.g. family, order) was used throughout this book. Genera (and spec...

Sahu, SC & Casciano, DA 2014, Handbook of Nanotoxicology, Nanomedicine and Stem Cell Use in Toxicology, Wiley.
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The Handbook of Nanotoxicology, Nanomedicine and Stem Cell Use in Toxicology provides an insight into the current trends and future directions of research in these rapidly developing scientific fields.

Aharonovich, I & Babinec, T 2014, 'Single Color Centers in Diamond' in Sarin, VK (ed), Comprehensive Hard Materials, Elsevier, pp. 469-491.
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Photonic technologies play key roles in twenty-first century technologies. In addition to their traditional optical communications, quantum photonics, which relies on single photon emitters, offers new approaches to information processing. In this chapter, we discuss the photophysical properties and applications of single defects in diamond-also known as color centers. Although the focus will be on one particular emitter-the nitrogen-vacancy center, other defects will be mentioned and reviewed. Promising applications, namely, photonic devices and magnetometry, will be discussed in more detail, highlighting the recent literature. Finally, an outlook for diamond photonics will be presented. © 2014 Elsevier Ltd. All rights reserved.

Aharonovich, I & Prawer, S 2014, 'Promising directions in diamond technologies for quantum information processing (QIP) and sensing' in Quantum Information Processing with Diamond, Elsevier, pp. 307-317.
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© 2014 Elsevier Ltd. All rights reserved. This final chapter summarizes some of the emerging topics in the usage of diamond for quantum information processing. Practical applications include biosensing and bioimaging using colour centres in diamond, as well as pathways towards integrated quantum photonics using diamond as a platform. On the other hand, challenges will be discussed, including surface terminations and engineering new, superior optically active defects. Finally, we discuss the outlook for the field of quantum information processing (QIP) with diamond.

Choi, AH, Ben-Nissan, B, Conway, RC & Macha, IJ 2014, 'Advances in Calcium Phosphate Nanocoatings and Nanocomposites' in Ben-Nissan, B (ed), Springer Series in Biomaterials Science and Engineering, Springer Berlin Heidelberg, Germany, pp. 485-509.
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It is possible by using nanocomposite approach to control the strength and Young’s modulus of the composite to become close to those of human cortical or cancellous bone. This is made possible with the help of secondary substitution phases. Various materials have been applied as biomaterials and tissue regeneration materials, and the in vivo cytotoxicity and biocompatibility have been the main consideration in their use and their long-term success. This chapter aims to give a brief introduction and current applications of calcium phosphate nanocomposites as tissue engineering and as a delivery vehicle for drugs, genes, and proteins. Furthermore, the chapter will also examine the potential use of calcium phosphate nanocomposite coatings for tissue engineering scaffolds.

Choi, AH, Heness, G & Ben-Nissan, B 2014, 'Using finite element analysis (FEA) to understand the mechanical properties of ceramic matrix composites' in Low, J (ed), Advances in Ceramic Matrix Composites, Elsevier, Cambridge, pp. 286-311.
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Chou, J, Hao, J, Ben-Nissan, B, Milthorpe, B & Otsuka, M 2014, 'Calcium Phosphate Derived from Foraminifera Structures as Drug Delivery Systems and for Bone Tissue Engineering' in Springer Series in Biomaterials Science and Engineering, Springer Berlin Heidelberg, pp. 415-433.
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Cortie, MB, Stokes, NL, Heness, GL & Smith, G 2014, 'Nanotechnology for Sustainable Manufacturing' in Rickerby, D (ed), Nanotechnology for Sustainable Manufacturing, CRC Press, USA.
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Craddock, M 2014, 'On an Integral Arising in Mathematical Finance' in Dieci, R, He, XZ & Hommes, C (eds), Nonlinear Economic Dynamics and Financial Modelling, Springer International Publishing, Germany, pp. 355-370.
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We consider an integral which arises in several problems in analysis and financial mathematics. We significantly simplify the integral, yielding a tractable form which is more useful for explicit calculations.

Fujimoto, R, Sasaki, T, Ishikawa, R, Osabe, K, Kawanabe, T & Dennis, ES 2014, 'The Role of Bioinformatics in Agriculture' in Kumar, S (ed), The Role of Bioinformatics in Agriculture, Apple Academic Press, pp. 327-356.
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© 2014 by Apple Academic Press, Inc. Variation in DNA sequence can cause variation in gene expression, which influences quantitative phenotypic variation in organisms and is an important factor in natural variation. Gene expression regulatory networks are comprised of cis-and trans-acting factors, and differences in gene expression are attributable to genetic variation. In eukaryotes, the genome is compacted into chromatin, and the chromatin structure plays an important role in gene expression: Gene expression can be controlled by changes in the structure of chromatin without changing the DNA sequence, and this phenomenon is termed “epigenetic” control. Recently, there have been many reports indicating that epigenetic change can cause phenotypic variation, and thus epigenetic change can be considered as an important factor in understanding phenotypic change. DNA methylation and histone modifications are well known epigenetic modifications. DNA methylation refers to an addition of a methyl group at the fifth carbon position of a cytosine ring, and in plants it is observed not only in the symmetric CG context but also in sequence contexts of CHG and CHH (where H is A, C, or T) [1-3]. DNA methylation is enriched in heterochromatic regions, such as in centromeric and pericentromeric regions, predominantly consisting of transposons [3-7]. Most transposons are immobile to protect genome integrity and are silenced via DNA methylation [3,8-12]. DNA methylation is also observed in euchromatic regions such as gene-coding regions (gene body methylation), and it is widely seen in eukaryotes [3,13,14].

Geider, RJ, Moore, CM & Suggett, DJ 2014, 'Ecology of Marine Phytoplankton' in Ecology and the Environment, Springer New York, pp. 483-531.
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George, AM & Jones, PM 2014, 'Bacterial ABC Transporters: Structure and Function' in Han Renaut (ed), Bacterial Membranes: Structural and Molecular Biology, Horizon Scientific Press, Norwich, UK.
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ATP-Binding-Cassette (ABC) membrane transporters belong to one of the largest and most ancient gene families, occurring in bacteria, archaea, and eukaryota. In addition to nutrient uptake, ABC transporters are involved in other diverse processes such as the export of toxins, peptides, proteins, antibiotics, polysaccharides and lipids, and in cell division, bacterial immunity and nodulation in plants. While prokaryotic ABC transporters encompass both importers and exporters, eukaryotes harbour only exporters. Bacterial ABC transporters are intricately involved either directly or indirectly in all aspects of cellular physiology, metabolism, homeostasis, drug resistance, secretion, and cellular division. Whilst several complete ABC transporter structures have been solved over the past decade, their functional mechanism of transport is still somewhat controversial and this aspect is discussed in detail.

Glenn, EP, Nagler, PL & Huete, AR 2014, 'Change Detection Using Vegetation Indices and Multiplatform Satellite Imagery at Multiple Temporal and Spatial Scales' in Weng, Q (ed), Scale Issues in Remote Sensing, Wiley, USA, pp. 79-107.
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© 2014 by John Wiley & Sons, Inc. All rights reserved. This chapter describes emerging methods for using satellite imagery across temporal and spatial scales using a case study approach to illustrate some of the opportunities now available for combining observations across scales. It explores the use of multiplatform sensor systems to characterize ecological change, as exemplified by efforts to scale the effects of a biocontrol insect (the leaf beetle Diorhabda carinulata) on the phenology and water use of Tamarix shrubs (Tamarix ramosissima and related species and hybrids) targeted for removal on western U.S. rivers, from the level of individual leaves to the regional level of measurement. Finally, the chapter summarizes the lessons learned and emphasize the need for ground data to calibrate and validate remote sensing data and the types of errors inherent in scaling point data over wide areas, illustrated with research on evapotranspiration (ET) of Tamarix using a wide range of ground measurement and remote sensing methods.

Godfree, RC & Murray, BR 2014, 'Invasive Species: Plants' in Van Alfen, NK (ed), Encyclopedia of Agriculture and Food Systems, Elsevier, San Diego, pp. 66-77.
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© 2014 Elsevier Inc. All rights reserved. Invasive plant species impact on natural and agroecosystems on a global scale. Understanding and managing such species is a rapidly evolving area of research that integrates the disciplines of ecology, evolutionary biology, and ecophysiology. This article provides an overview of invasion biology, focusing on the nature of the invasion pathway and key processes that lead to ecosystem impact. Key principles are investigated further through discussion of the impacts of transgenic organisms on weed pressure, and likely future synergisms between climate change and invasive species. Comparative analysis of historical invasion patterns and other avenues for future research are also identified.

Gupta, V, Thakur, RS, Baghel, RS, Reddy, CRK & Jha, B 2014, 'Seaweed Metabolomics' in Bourgougnon, N (ed), Advances in Botanical Research, Elsevier, pp. 31-52.
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Harder, T, Rice, SA, Dobretsov, S, Thomas, T, Carré‐Mlouka, A, Kjelleberg, S, Steinberg, PD & McDougald, D 2014, 'Bacterial Communication Systems' in La Barre, S & Komprobst, JM (eds), Outstanding Marine Molecules, Wiley, USA, pp. 171-188.
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Like multicellular organisms, bacteria can regulate gene expression at the multicellular level. The coordination of multicellular bacterial behavior occurs via a chemically mediated process known as quorum sensing (QS). Currently, there are five well-defined classes of chemical signals in bacteria that support the concept of QS. By coupling an extracellular bacterial signal with gene expression, bacteria can control gene expression in such a way that the majority of the population expresses the same phenotype simultaneously. In this chapter, the molecular mechanisms of QS, the effective range of QS-regulated processes, and the ecological role of quorum quenching, namely the inhibition of QS, are discussed. QS occurs most frequently in bacterial species that associate with surfaces or higher organisms, either as a pathogen or as a beneficial associate. Three seminal examples of QS-mediated cross-kingdom signaling in the marine environment are reviewed: (i) the chemical defense of the red seaweed Delisea pulchra; (ii) the mutualistic association of Vibrio fischeri with the Hawaiian bobtail squid; and (iii) the exploitation of bacterial QS during settlement of marine spores and invertebrate larvae.

Hsu, AC-Y, Loo, S-L, Aghdam, FF, Parsons, K, Hansbro, PM & Wark, PAB 2014, 'Airway Epithelial and Early Innate Immune Responses toVirus Infections' in Human Respiratory Viral Infections, CRC Press, pp. 29-44.
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Huete, A 2014, 'Soil Properties' in Encyclopedia of Earth Sciences Series, Springer New York, pp. 788-791.
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Huete, A 2014, 'Vegetation Indices' in Encyclopedia of Earth Sciences Series, Springer New York, pp. 883-886.
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Huete, A, Miura, T, Yoshioka, H, Ratana, P & Broich, M 2014, 'Indices of Vegetation Activity' in Springer Remote Sensing/Photogrammetry, Springer Berlin Heidelberg, pp. 1-41.
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Idrees, S 2014, 'Journey of Protein from Sequence to Structure: An Innovative Bioinformatics Approach' in Biotechnology, Studium Press LLC, U.S.A., Houston, TX 77072 - U.S.A., pp. 129-142.

Idrees, S 2014, 'RNA Interference as a Therapeutic StrategyAgainst Viral Diseases' in Biotechnology, pp. 369-387.

Jin, D, Lu, Y, Leif, RC, Yang, S, Rajendran, M & Miller, LW 2014, 'How to Build a Time‐Gated Luminescence Microscope' in Current Protocols in Cytometry, Wiley, USA.
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AbstractThe sensitivity of filter‐based fluorescence microscopy techniques is limited by autofluorescence background. Time‐gated detection is a practical way to suppress autofluorescence, enabling higher contrast and improved sensitivity. In the past few years, three groups of authors have demonstrated independent approaches to build robust versions of time‐gated luminescence microscopes. Three detailed, step‐by‐step protocols are provided here for modifying standard fluorescent microscopes to permit imaging time‐gated luminescence. Curr. Protoc. Cytom. 67:2.22.1‐2.22.36. © 2014 by John Wiley & Sons, Inc.

Lazenby, JJ & Chang, CY 2014, 'Pathogens' in Medical Sciences at a Glance, John Wiley & Sons, USA, pp. 130-133.
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The definitive companion for medical science study and revision Medical Sciences at a Glance consolidates the scientific knowledge a student needs to know to provide a solid framework of key facts to build on.

Macmillan, A, Cranfield, C & Martinac, B 2014, 'Fluorescence Methods for Monitoring Mechanosensitive Channels' in Handbook of Imaging in Biological Mechanics, CRC Press, pp. 425-432.
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Macmillan, A, Cranfield, CG & Martinac, B 2014, 'Handbook of Imaging in Biological Mechanics' in Neu, CP & Genin, GM (eds), Handbook of Imaging in Biological Mechanics, CRC Press, pp. 425-431.
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Over the last 10 to 15 years, fluorescence methods have become frequently used for studies of the conformational changes of various membrane proteins including ion channels that function as gated membrane pores in numerous physiological processes essential for the normal function of biological cells. In combination with molecular biological methods that allow introduction of fluorescent labeling in vivo and in vitro, and functional electrophysiological voltage- and patch-clamp recording techniques, fluorescence spectroscopy methods, such as Förster resonance energy transfer (FRET), have made ion channel proteins accessible to studies of protein structure and function relationship. Here we focus on the use of these methods in studies of structural dynamics of bacterial mechanosensitive channels, which to date are among the best studied membrane channels functioning in mechanosensory transduction in living cells.

Novikov, AA, Ling, TG & Kordzakhia, N 2014, 'Pricing of Volume-Weighted Average Options: Analytical Approximations and Numerical Results' in Kabanov, Y, Rutkowski, M & Zariphopoulou, T (eds), Inspired by Finance, Springer International Publishing, London, pp. 461-474.
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© Springer International Publishing Switzerland 2014. All rights are reserved. The volume weighted average price (VWAP) over rolling number of days in the averaging period is used as a benchmark price by market participants and can be regarded as an estimate for the price that a passive trader will pay to purchase securities in a market. The VWAP is commonly used in brokerage houses as a quantitative trading tool and also appears in Australian taxation law to specify the price of share-buybacks of publically-listed companies. Most of the existing literature on VWAP focuses on strategies and algorithms to acquire market securities at a price as close as possible to VWAP. In our setup the volume process is modeled via a shifted squared Ornstein-Uhlenbeck process and a geometric Brownian motion is used to model the asset price. We derive the analytical formulae for moments of VWAP and then use the moment matching approach to approximate a distribution of VWAP. Numerical results for moments of VWAP and call-option prices have been verified by Monte Carlo simulations.

Ryan, LM 2014, 'Reflections on diversity' in Past, Present, and Future of Statistical Science, pp. 229-234.
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I recall quite vividly the start in the early 1990s of my interest in fostering diversity in higher education. Professor James Ware had just been appointed as the Academic Dean at Harvard School of Public Health and was letting go of some of his departmental responsibilities. He asked if I would take over as director of the department’s training grant in environmental statistics, funded through the National Institute of Environmental Health Sciences (NIEHS). Being an ambitious young associate professor, I eagerly accepted. It wasn’t long before I had to start preparing the grant’s competitive renewal. These were the days when funding agencies were becoming increasingly proactive in terms of pushing Universities on the issue of diversity and one of the required sections in the renewal concerned minority recruitment and retention. Not knowing much about this, I went for advice to the associate dean for student affairs, a bright and articulate African American woman named Renee (not her true name). When I asked her what the School was doing to foster diversity, she chuckled and said “not much!” She suggested that I let her know when I was traveling to another city and she would arrange for me to visit some colleges with high minority enrollments so that I could engage with students and teachers to tell them about opportunities for training in biostatistics at Harvard.

Turnbull, L & Whitchurch, CB 2014, 'Motility Assay: Twitching Motility' in Filloux, A & Ramos, JL (eds), Pseudomonas Methods and Protocols, Springer New York, New York, pp. 73-86.
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Twitching motility is a mode of solid surface translocation that occurs under humid conditions on semisolid or solid surfaces, is dependent on the presence of retractile type IV pili and is independent of the presence of a flagellum. Surface translocation via twitching motility is powered by the extension and retraction of type IV pili and can manifest as a complex multicellular collective behavior that mediates the active expansion of colonies cultured on the surface of solidified nutrient media, and of interstitial colonies that are cultured at the interface between solidified nutrient media and an abiotic material such as the base of a petri dish or a glass coverslip. Here we describe two methods for assaying twitching motility mediated interstitial colony expansion in P. aeruginosa. The first method, the Macroscopic Twitching Assay, can be used to determine if a strain is capable of twitching motility mediated interstitial colony expansion and can also be used to quantitatively assess the influence of mutation or environmental signals on this process. The second method, the Microscopic Twitching Assay, can be used for detailed interrogation of the movements of individual cells or small groups of bacteria during twitching motility mediated colony expansion.

Webb, JK, Harlow, PS & Pike, DA 2014, 'Australian reptiles and their conservation' in Stow, A, Maclean, N & Holwell, GI (eds), Austral Ark, Cambridge University Press, UK, pp. 354-381.
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© Cambridge University Press 2015. Australia has a spectacular and diverse reptile fauna approaching 1000 species, 93% of which are endemic to the continent. Despite this, there is a paucity of information on the biology of Australian reptiles compared with mammals and birds. The single greatest threat to Australian reptiles is the removal of native vegetation, most of which has occurred in the state of Queensland during the past few decades. Since European settlement in Australia, land clearing for stock grazing and other agricultural activities has reduced the extent of native vegetation, and resulted in extensive habitat fragmentation. Ultimately, habitat fragmentation leads to species loss and local extinctions. Other threats to Australian reptiles include livestock grazing, which occurs on 55% of the continent, coupled with changing fire regimes and predation by exotic predators, especially foxes and feral cats. Currently, we know little about the long-term impacts of pastoralism, fire and introduced predators on reptile communities. The conservation of Australian reptiles requires urgent changes in government policy to reduce rates of vegetation clearing. A critical challenge is the conservation of reptiles in the vast arid and semi-arid regions, where reptile diversity is remarkably high. This will require coordinated management of threatening processes across multiple land tenures, including pastoral leases, crown lands, Aboriginal lands and conservation reserves. In southern Australia, the conservation of reptiles in fragmented landscapes will require strategic tree planting to increase the sizes of habitat remnants and their connectivity, in addition to retaining important structural habitat features such as rock outcrops, old growth trees and fallen timber. In addition to in situ conservation practices, breeding programmes are being employed to prevent the extinction of imperilled species.

Wensink, H & Alpers, W 2014, 'SAR-Based Bathymetry' in Encyclopedia of Earth Sciences Series, Springer New York, pp. 719-722.
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Abboud, M, Gordon-Thomson, C, Hoy, AJ, Balaban, S, Rybchyn, MS, Cole, L, Su, Y, Brennan-Speranza, TC, Fraser, DR & Mason, RS 2014, 'Uptake of 25-hydroxyvitamin D by muscle and fat cells', The Journal of Steroid Biochemistry and Molecular Biology, vol. 144, pp. 232-236.
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Adams, PN, Aldridge, A, Vukman, KV, Donnelly, S & O'Neill, SM 2014, 'Fasciola hepatica tegumental antigens indirectly induce an M2 macrophage-like phenotype in vivo', PARASITE IMMUNOLOGY, vol. 36, no. 10, pp. 531-539.
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© 2014 John Wiley & Sons Ltd. The M2 subset of macrophages has a critical role to play in host tissue repair, tissue fibrosis and modulation of adaptive immunity during helminth infection. Infection with the helminth, Fasciola hepatica, is associated with M2 macrophages in its mammalian host, and this response is mimicked by its excretory-secretory products (FhES). The tegumental coat of F. hepatica (FhTeg) is another major source of immune-modulatory molecules; we have previously shown that FhTeg can modulate the activity of both dendritic cells and mast cells inhibiting their ability to prime a Th1 immune response. Here, we report that FhTeg does not induce Th2 immune responses but can induce M2-like phenotype in vivo that modulates cytokine production from CD4+ cells in response to anti-CD3 stimulation. FhTeg induces a RELMα expressing macrophage population in vitro, while in vivo, the expression of Arg1 and Ym-1/2 but not RELMα in FhTeg-stimulated macrophages was STAT6 dependent. To support this finding, FhTeg induces RELMα expression in vivo prior to the induction of IL-13. FhTeg can induce IL-13-producing peritoneal macrophages following intraperitoneal injection This study highlights the important role of FhTeg as an immune-modulatory source during F. hepatica infection and sheds further light on helminth-macrophage interactions.

Adlard, PA, Sedjahtera, A, Gunawan, L, Bray, L, Hare, D, Lear, J, Doble, P, Bush, AI, Finkelstein, DI & Cherny, RA 2014, 'A novel approach to rapidly prevent age-related cognitive decline', AGING CELL, vol. 13, no. 2, pp. 351-359.
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Summary: The loss of cognitive function is a pervasive and often debilitating feature of the aging process for which there are no effective therapeutics. We hypothesized that a novel metal chaperone (PBT2; Prana Biotechnology, Parkville, Victoria, Australia) would enhance cognition in aged rodents. We show here that PBT2 rapidly improves the performance of aged C57Bl/6 mice in the Morris water maze, concomitant with increases in dendritic spine density, hippocampal neuron number and markers of neurogenesis. There were also increased levels of specific glutamate receptors (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid and N-methyl-d-aspartate), the glutamate transporter (VGLUT1) and glutamate itself. Markers of synaptic plasticity [calmodulin-dependent protein kinase II (CaMKII) and phosphorylated CaMKII, CREB, synaptophysin] were also increased following PBT2 treatment. We also demonstrate that PBT2 treatment results in a subregion-specific increase in hippocampal zinc, which is increasingly recognized as a potent neuromodulator. These data demonstrate that metal chaperones are a novel approach to the treatment of age-related cognitive decline. © 2013 The Authors. Aging Cell published by the Anatomical Society and John Wiley & Sons Ltd.

Afzal, S, Daoud, WA & Langford, SJ 2014, 'Exploring the Use of Dye‐Sensitisation by Visible‐Light as New Approach to Self‐Cleaning Textiles', Journal of the Chinese Chemical Society, vol. 61, no. 7, pp. 757-762.
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AbstractPhotocatalytic degradation of organic contaminants by self‐cleaning textiles is an efficient method to create green environment and minimise energy consumption. In this work, the concept of dye‐sensitised self‐cleaning textiles has been introduced by incorporating monolayers of meso‐tetra(4‐carboxyphenyl)porphyrin (TCPP) on the surface of titania‐coated cotton against methylene blue. Different complexes of TCPP (M = 2H, Fe, Co, Zn, Cu) have been trialled and evaluated for photocatalytic activity and stability. Cotton fabrics coated with TCPP show superior photochemical activity as compared to TiO2‐coated fabrics under visible‐light irradiation. The free base derivative availed the highest photocatalytic efficiency when compared to the metal complexes with Cu∼Fe > Co > Zn. In terms of stability, meso‐tetra(4‐car‐boxyphenyl)porphyrinato copper(II) showed significant stabilisation under photocatalytic conditions when compared to the metal‐free porphyrin and other metal complexes (Cu ≫ Co > 2H > Zn∼Fe). Porphyrins offer great potential in visible‐light self‐cleaning applications.

Aharonovich, I 2014, 'Diamond nanocrystals for photonics and sensing', JAPANESE JOURNAL OF APPLIED PHYSICS, vol. 53, no. 5.
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Fluorescent nanodiamonds (FNDs) are becoming a pivotal material in a variety of applications spanning sensing, bio-labeling and nanophotonics. The unique feature of these nanoparticles is their ability to host bright, optically active, photostable defects (color centers) that emit across the entire spectral range. In conjunction with their chemical stability and the relatively known carbon chemistry, nanodiamonds are becoming a key player in modern technologies. This brief review will highlight some of the recent advances of FNDs with an emphasis on nanophotonics. © 2014 The Japan Society of Applied Physics.

Aharonovich, I 2014, 'Silicon magic', Nature Photonics, vol. 8, no. 11, pp. 818-819.
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© 2014 Macmillan Publishers Limited. All rights reserved. Silicon is the material of choice for modern microelectronics, whereas diamond is a luxurious gem. Now, researchers have demonstrated that silicon impurities in diamond can generate indistinguishable single photons-a requirement for quantum photonics and computing.

Aharonovich, I & Neu, E 2014, 'Diamond Nanophotonics', Advanced Optical Materials, vol. 2, no. 10, pp. 911-928.
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The burgeoning field of nanophotonics has grown to be a major research area,primarily because of the ability to control and manipulate single quantumsystems (emitters) and single photons on demand. For many years studyingnanophotonic phenomena was limited to traditional semiconductors (includingsilicon and GaAs) and experiments were carried out predominantly at cryogenictemperatures. In the last decade, however, diamond has emerged as a newcontender to study photonic phenomena at the nanoscale. Offering plethora ofquantum emitters that are optically active at room temperature and ambientconditions, diamond has been exploited to demonstrate super-resolutionmicroscopy and realize entanglement, Purcell enhancement and other quantum andclassical nanophotonic effects. Elucidating the importance of diamond as amaterial, this review will highlight the recent achievements in the field ofdiamond nanophotonics, and convey a roadmap for future experiments andtechnological advancements.

Ahmed, M, Yajadda, MMA, Han, ZJ, Su, D, Wang, G, Ostrikov, KK & Ghanem, A 2014, 'Single-walled carbon nanotube-based polymer monoliths for the enantioselective nano-liquid chromatographic separation of racemic pharmaceuticals', Journal of Chromatography A, vol. 1360, pp. 100-109.
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Single-walled carbon nanotubes were encapsulated into different polymer-based monolithic backbones. The polymer monoliths were prepared via the copolymerization of 20% monomers, glycidyl methacrylate, 20% ethylene glycol dimethacrylate and 60% porogens (36% 1-propanol, 18% 1,4-butanediol) or 16.4% monomers (16% butyl methacrylate, 0.4% sulfopropyl methacrylate), 23.6% ethylene glycol dimethacrylate and 60% porogens (36% 1-propanol, 18% 1,4-butanediol) along with 6% single-walled carbon nanotubes aqueous suspension. The effect of single-walled carbon nanotubes on the chiral separation of twelve classes of pharmaceutical racemates namely; α- and β-blockers, antiinflammatory drugs, antifungal drugs, dopamine antagonists, norepinephrine-dopamine reuptake inhibitors, catecholamines, sedative hypnotics, diuretics, antihistaminics, anticancer drugs and antiarrhythmic drugs was investigated. The enantioselective separation was carried out under multimodal elution to explore the chiral recognition capabilities of single-walled carbon nanotubes using reversed phase, polar organic and normal phase chromatographic conditions using nano-liquid chromatography. Baseline separation was achieved for celiprolol, chlorpheniramine, etozoline, nomifensine and sulconazole under multimodal elution conditions. Satisfactory repeatability was achieved through run-to-run, column-to-column and batch-to-batch investigations. Our findings demonstrate that single-walled carbon nanotubes represent a promising stationary phase for the chiral separation and may open the field for a new class of chiral selectors. © 2014 .

Aili, SR, Touchard, A, Escoubas, P, Padula, MP, Orivel, J, Dejean, A & Nicholson, GM 2014, 'Diversity of peptide toxins from stinging ant venoms', TOXICON, vol. 92, pp. 166-178.
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© 2014 Elsevier Ltd. All rights reserved. Ants (Hymenoptera: Formicidae) represent a taxonomically diverse group of arthropods comprising nearly 13,000 extant species. Sixteen ant subfamilies have individuals that possess a stinger and use their venom for purposes such as a defence against predators, competitors and microbial pathogens, for predation, as well as for social communication. They exhibit a range of activities including antimicrobial, haemolytic, cytolytic, paralytic, insecticidal and pain-producing pharmacologies. While ant venoms are known to be rich in alkaloids and hydrocarbons, ant venoms rich in peptides are becoming more common, yet remain understudied. Recent advances in mass spectrometry techniques have begun to reveal the true complexity of ant venom peptide composition. In the few venoms explored thus far, most peptide toxins appear to occur as small polycationic linear toxins, with antibacterial properties and insecticidal activity. Unlike other venomous animals, a number of ant venoms also contain a range of homodimeric and heterodimeric peptides with one or two interchain disulfide bonds possessing pore-forming, allergenic and paralytic actions. However, ant venoms seem to have only a small number of monomeric disulfide-linked peptides. The present review details the structure and pharmacology of known ant venom peptide toxins and their potential as a source of novel bioinsecticides and therapeutic agents.

Ajani, PA, Allen, AP, Ingleton, T & Armand, L 2014, 'A decadal decline in relative abundance and a shift in microphytoplankton composition at a long‐term coastal station off southeast Australia', Limnology and Oceanography, vol. 59, no. 2, pp. 519-531.
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In this study, we examined 11 yr (1998–2009) of water samples collected from Port Hacking coastal monitoring station 8 km offshore from Sydney, Australia, to assess changes in the microphytoplankton in relation to climate‐related trends in environmental variables. A total of 152 taxa (85 genera) were identified, with the small diatom Thalassiosira cf. partheneia and the tropical cyanobacterium Trichodesmium erythraeum being the dominant species over the past decade. Taxon richness showed a distinct seasonal pattern, peaking in the austral winter. Ordination analyses revealed significant seasonal and interannual trends in species composition, including a decadal decline in dinoflagellates relative to diatoms toward the present. This decadal shift in taxonomic composition was, in turn, significantly associated with declines in water temperatures over this time period. Total abundance varied by 12 orders of magnitude (8.5 × 10−8 to 7.4 × 104 cells L−1), with values separable into bloom and nonbloom regimes at an abundance threshold of 7.1 × 10−5 cells L−1. Significant temporal declines in abundance were observed during both bloom and nonbloom regimes. Blooms occurred most consistently in March, September, and December.

Ajani, PA, Allen, AP, Ingleton, T & Armand, L 2014, 'Erratum: A decadal decline in relative abundance and a shift in microphytoplankton composition at a long‐term coastal station off southeast Australia', Limnology and Oceanography, vol. 59, no. 6, pp. 2240-2242.
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Alejandro Dinamarca, M, Orellana, L, Aguirre, J, Baeza, P, Espinoza, G, Canales, C & Ojeda, J 2014, 'Biodesulfurization of dibenzothiophene and gas oil using a bioreactor containing a catalytic bed with Rhodococcus rhodochrous immobilized on silica', Biotechnology Letters, vol. 36, no. 8, pp. 1649-1652.
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Aliev, G, Shahida, K, Gan, S, Firoz, CK, Khan, A, Abuzenadah, A, Kamal, W, Kamal, M, Tan, Y, Qu, X & Reale, M 2014, 'Alzheimer Disease and Type 2 Diabetes Mellitus: The Link to Tyrosine Hydroxylase and Probable Nutritional Strategies', CNS & Neurological Disorders - Drug Targets, vol. 13, no. 3, pp. 467-477.
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Alzheimer disease (AD) and type 2 diabetes mellitus (T2DM) are chronic health disorders that affect millions of people around the world. According to recent studies, there are molecular similarities in the inflammatory pathways involved in both AD and T2DM, which opens a new avenue for researchers with different perspectives to target the cause of these diseases rather than their obvious symptoms. Several links between inflammation, cardiovascular disease, T2DM and central nervous system disorders such as AD and Parkinson's disease have been elucidated. Mutations in the hippocampal-β-amyloid precursor protein gene in genetically high-risk individuals have been shown to cause the early onset of AD symptoms. The overexpression of β-amyloid protein in the hippocampal region and the synaptotoxicity that occurs as a result have been considered a typical feature of AD and leads to neuronal loss and cognitive decline. However, the identity of the cellular components that cause the late onset of the disease seen in the majority of the cases is still unknown. Synaptic insults associated with neuronal dysfunction may involve several cascades and molecules, one of which has been hypothesized to be tyrosine hydroxylase (TH). The axons of the noradrenergic cells that project to the hippocampus appear to be affected by the β-amyloid protein, which subsequently contributes to TH loss in Alzheimer brain cells. In this review, we attempt to shed light on the important mechanisms involved in AD as well as T2DM such as inflammatory factors, abnormalities in the insulin signaling system and the possible role of the endocrine enzyme TH.

Alkhouri, H, Poppinga, WJ, Tania, NP, Ammit, A & Schuliga, M 2014, 'Regulation of pulmonary inflammation by mesenchymal cells', Pulmonary Pharmacology & Therapeutics, vol. 29, no. 2, pp. 156-165.
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© 2014 Elsevier Ltd. Pulmonary inflammation and tissue remodelling are common elements of chronic respiratory diseases such as asthma, chronic obstructive pulmonary disease (COPD), idiopathic pulmonary fibrosis (IPF), and pulmonary hypertension (PH). In disease, pulmonary mesenchymal cells not only contribute to tissue remodelling, but also have an important role in pulmonary inflammation. This review will describe the immunomodulatory functions of pulmonary mesenchymal cells, such as airway smooth muscle (ASM) cells and lung fibroblasts, in chronic respiratory disease. An important theme of the review is that pulmonary mesenchymal cells not only respond to inflammatory mediators, but also produce their own mediators, whether pro-inflammatory or pro-resolving, which influence the quantity and quality of the lung immune response. The notion that defective pro-inflammatory or pro-resolving signalling in these cells potentially contributes to disease progression is also discussed. Finally, the concept of specifically targeting pulmonary mesenchymal cell immunomodulatory function to improve therapeutic control of chronic respiratory disease is considered.

Alkhouri, H, Rumzhum, NN, Rahman, MM, FitzPatrick, M, de Pedro, M, Oliver, BG, Bourke, JE & Ammit, AJ 2014, 'TLR2 activation causes tachyphylaxis to beta(2)-agonists in vitro and ex vivo: modelling bacterial exacerbation', ALLERGY, vol. 69, no. 9, pp. 1215-1222.
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Background Asthma is a widespread chronic health problem exacerbated by common viral and bacterial infections. Further research is required to understand how infection worsens asthma control in order to advance therapeutic options in the future. Recent research has revealed that β2- Adrenergic receptor (β2-AR) agonists lose bronchodilatory efficacy because the receptor-mediated molecular pathways responsible for their beneficial actions are desensitized by infection. To date, most studies have focussed on viral infection, leaving the impact of bacterial infection on β2-AR desensitization relatively under-investigated. We address this in this study. Methods and Results Utilizing an in vitro model of bacterial exacerbation in airway smooth muscle (ASM) cells, we show that activation of toll-like receptor 2 (TLR2; mimicking bacterial infection) in the presence of an inflammatory stimulus leads to β2-AR desensitization. This occurs via TLR2-dependent upregulation of cyclooxygenase 2 (COX-2) mRNA expression and increased secretion of PGE2. Importantly, PGE 2 causes heterologous β2-AR desensitization and reduces cAMP production in response to short-Acting (salbutamol) and long-Acting (formoterol) β2-Agonists. Thus, bacterial infectious stimuli act in a PGE2-dependent manner to severely curtail the beneficial actions of β2-Agonists. The impact of β2-AR desensitization is demonstrated by reduced gene expression of the critical anti-inflammatory molecule MKP-1 in response to β2-Agonists, as well as impaired bronchodilation in a mouse lung slices. Conclusions Taken together, our results show that, like viruses, bacteria induce prostanoid-dependent β2-AR desensitization on ASM cells. Notably, COX-2 inhibition with the specific inhibitor celecoxib represses PGE2 secretion, presenting a feasible pharmacological option for treatment of infectious exacerbation in asthma in the future. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Al-Odat, I, Chen, H, Chan, YL, Amgad, S, Wong, MG, Gill, A, Pollock, C & Saad, S 2014, 'The Impact of Maternal Cigarette Smoke Exposure in a Rodent Model on Renal Development in the Offspring', PLoS ONE, vol. 9, no. 7, pp. e103443-e103443.
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This study aimed to investigate whether maternal cigarette smoke exposure can disrupt fetal kidney development by changing the expression of growth and transcription factors essential for renal development, and thereafter predispose the offspring to chronic kidney disease later in life. Female Balb/c mice (6 weeks) were exposed either to cigarette smoke or air under identical conditions, 6 weeks prior to mating, during gestation and during lactation. Male offspring were sacrificed at three time points, postnatal day (P)1, P20 (weaning age), and 13 weeks (mature age). Blood, urine, and kidneys were collected for analysis. At P1, the developmental genes fibroblast growth factor 2, glial cell-line derived neurotrophic factor and paired box 2 were upregulated at mRNA and protein levels; whilst fibroblast growth factor (FGF) 7 and FGF10 were downregulated. At P20, mRNA expression of FGF2, FGF10 and Wingless-type 4 was upregulated by maternal smoke exposure. These changes were normalised in adulthood. Nephron development was delayed, with fewer nephron numbers from P1 persisted to adulthood; while glomerular volume was increased at P20 but reduced in adulthood. Pro-inflammatory marker monocyte chemoatractant protein 1 (MCP1) was increased in the kidney by maternal smoke exposure. These changes were accompanied by an increased albumin/creatinine ratio in adulthood, suggesting reduced renal dysfunction. In conclusion maternal cigarette smoke exposure prior to and during pregnancy, as well as lactation leads to significant renal underdevelopment and functional abnormalities in adulthood. This study confirms the hypothesis that maternal smoking predisposes offspring to chronic kidney disorders. © 2014 Al-Odat et al.

Anantachaisilp, S, Smith, SM, Ton-That, C, Osotchan, T, Moon, AR & Phillips, MR 2014, 'Tailoring Deep Level Surface Defects in ZnO Nanorods for High Sensitivity Ammonia Gas Sensing', JOURNAL OF PHYSICAL CHEMISTRY C, vol. 118, no. 46, pp. 27150-27156.
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© 2014 American Chemical Society. The influence of deep level surface defects on electrical and gas sensing properties of ZnO nanorods NH3(g) sensors was studied. ZnO nanorods 50-60 nm in diameter were synthesized via low-temperature hydrothermal growth at 90°C on sapphire substrates. The as-grown nanorods exhibited a cathodoluminescence (CL) peak centered at 1.90 eV (YL), attributed to LiZn deep acceptors or O interstitials. Subsequent annealing in O2 at 1 atm and Zn vapor at 650°C produced broad CL peaks centered at 1.70 eV (RL) and 2.44 eV (GL), respectively. The RL and GL have been ascribed to acceptor-like VZn and donor-like VO related centers, respectively. Electrical and gas sensing measurements established that the NH3 gas response sensitivity was 22.6 for O2 anneal (RL), 1.4 for Zn vapor anneal (GL), and 4.1 for the as-grown (YL) samples. Additionally, treatment in H-plasma quenched the RL and inverted the NH3 electrical response due to the incorporation of H donors. Changes in the gas sensing response are explained by a shift in the position of the ZnO Fermi level relative to the chemical potential of NH3 gas due to the creation of near surface donor or acceptors. These data confirm that ZnO nanorods arrays can be tailored to detect specific gas species. (Chemical Equation Presented).

Antonosyan, DA, Solntsev, AS & Sukhorukov, AA 2014, 'Effect of loss on photon-pair generation in nonlinear waveguide arrays', Physical Review A, vol. 90, no. 4.
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Antonosyan, DA, Solntsev, AS & Sukhorukov, AA 2014, 'Single-photon spontaneous parametric down-conversion in quadratic nonlinear waveguide arrays', Optics Communications, vol. 327, pp. 22-26.
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Ao, Z, Dou, S, Xu, Z, Jiang, Q & Wang, G 2014, 'Hydrogen storage in porous graphene with Al decoration', International Journal of Hydrogen Energy, vol. 39, no. 28, pp. 16244-16251.
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© 2014 Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved. Porous graphene and Al modified graphene have been reported to be promising hydrogen storage materials owing to their possible high hydrogen storage capacity. In this work, Al-decorated porous graphene is considered as hydrogen storage material, based on density functional calculations. It is found that the hydrogen storage capacity of the Al-decorated porous graphene is 10.5 wt%, with modest hydrogen adsorption energy from -1.11 to -0.41 eV/H2 to achieve efficient hydrogen storage/release at ambient conditions. In addition, hydrogen can be released gradually in three stages owing to different adsorption energy at different adsorption sites, which is desirable in actual hydrogen storage application. The mechanism for improving the hydrogen storage behavior by the decorated Al atom and its porosity is understood through analyzing the atomic charges, electronic distribution, and density of states of the system.

Apps, MG, Ammit, AJ, Gu, A & Wheate, NJ 2014, 'Analysis of montmorillonite clay as a vehicle in platinum anticancer drug delivery', Inorganica Chimica Acta, vol. 421, pp. 513-518.
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As a proof-of-concept study, the platinum anticancer complex [(1,10-phenanthroline)(1S,2S-diaminocyclohexane)platinum(II)]chloride, PHENSS, was loaded into montmorillonite (MMT) clay to evaluate its utility as a drug delivery vehicle. Loading is complete within one hour and the total amount of PHENSS that can be loaded into the clay is based on the PHENSS solution concentration in which the MMT is suspended. From a PHENSS solution concentration of 30 mM, a maximum loading of 0.257 mmol per gram of MMT can be achieved. The pH of the solution also has an effect with a solution pH of 6 giving maximum loading of PHENSS. Metal complex release from the MMT was examined using the dialysis bag and dispersion methods. PHENSS is incompletely released from MMT; after 4 h just 47% has been released from the clay using the dialysis method and 30% using the dispersion method. The release is also very fast with a half-life of just 10-16 min. The MMT was shown to have a negative effect on the in vitro cytotoxicity of PHENSS in the human breast cancer cell lines MCF-7 and MDA-MB-231, presumably due to the incomplete release of the metal complex from the clay. Overall the results demonstrate that MMT is not a suitable slow release vehicle for PHENSS, although it may still be of use to other platinum complexes and drugs. © 2014 Elsevier B.V. All rights reserved.

Arnold, M, Blaber, M & Ford, M 2014, 'Local plasmon resonances of metal-in-metal core-shells', OPTICS EXPRESS, vol. 22, no. 3, pp. 3186-3198.
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Arundel, J, Oxley, PR, Faiz, A, Crawford, J, Winter, S & Oldroyd, BP 2014, 'Remarkable uniformity in the densities of feral honey bee Apis mellifera Linnaeus, 1758 (Hymenoptera: Apidae) colonies in South Eastern Australia', Austral Entomology, vol. 53, no. 3, pp. 328-336.
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AbstractIt is often assumed that the density of feral honey bee colonies in Australia is sufficient to provide adequate pollination services to the many agricultural crops that require pollination. In contrast, there is concern that the density of feral colonies is sufficiently high to have inimical effects on Australian biota. For both these reasons, it is desirable to have robust estimates of the density of feral honey bee colonies in Australian landscapes. In this study, we mated four to five queens with wild drones at disturbed and undisturbed sites in three of the major ecosystems in Victoria Australia and examined the paternities of worker offspring to estimate the density of feral colonies within mating range of the test queens. We show that the density of feral colonies differs little with land use (cleared or uncleared) and is similar across the state. Our data suggest that the density of feral colonies is probably insufficient to provide adequate pollination of agricultural crops and that neither land use nor local climate variation is a major factor determining density. Finally, our data suggest that the mating range sampled by test queens is significantly greater than previously assumed.

Aryanfar, I, Wolff, C, Steel, MJ, Eggleton, BJ & Poulton, CG 2014, 'Mode conversion using stimulated Brillouin scattering in nanophotonic silicon waveguides', Optics Express, vol. 22, no. 23, pp. 29270-29270.
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© 2014 Optical Society of America We theoretically and numerically investigate Stimulated Brillouin Scattering generated mode conversion in high-contrast suspended silicon nanophotonic waveguides. We predict significantly enhanced mode conversion when the linked effects of radiation pressure and motion of the waveguide boundaries are taken into account. The mode conversion is more than 10 times larger than would be predicted if the effect of radiation pressure is not taken into account: we find a waveguide length of 740 μm is required for 20dB of mode conversion, assuming a total pump power of 1W. This is sufficient to bring the effect into the realm of chip-scale photonic waveguides. We explore the interaction between the different types of acoustic modes that can exist within these waveguides, and show how the presence of these modes leads to enhanced conversion between the different possible optical modes.

Asatryan, AA, Botten, LC, Fang, K, Fan, S & McPhedran, RC 2014, 'Two-dimensional Green's tensor for gyrotropic clusters composed of circular cylinders', JOURNAL OF THE OPTICAL SOCIETY OF AMERICA A-OPTICS IMAGE SCIENCE AND VISION, vol. 31, no. 10, pp. 2294-2303.
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Ashfaq, UA 2014, 'Medicinal plants against hepatitis C virus', World Journal of Gastroenterology, vol. 20, no. 11, pp. 2941-2941.
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Ashourloo, D, Mobasheri, MR & Huete, A 2014, 'Developing Two Spectral Disease Indices for Detection of Wheat Leaf Rust (Pucciniatriticina)', REMOTE SENSING, vol. 6, no. 6, pp. 4723-4740.
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Spectral vegetation indices (SVIs) have been widely used to detect different plant diseases. Wheat leaf rust manifests itself as an early symptom with the leaves turning yellow and orange. The sign of advancing disease is the leaf colour changing to brown while the final symptom is when the leaf becomes dry. The goal of this work is to develop spectral disease indices for the detection of leaf rust. The reflectance spectra of the wheat's infected and non-infected leaves at different disease stages were collected using a spectroradiometer. As ground truth, the ratio of the disease-affected area to the total leaf area and the fractions of the different symptoms were extracted using an RGB digital camera. Fractions of the various disease symptoms extracted by the digital camera and the measured reflectance spectra of the infected leaves were used as input to the spectral mixture analysis (SMA). Then, the spectral reflectance of the different disease symptoms were estimated using SMA and the least squares method. The reflectance of different disease symptoms in the 450~1000 nm were studied carefully using the Fisher function. Two spectral disease indices were developed based on the reflectance at the 605, 695 and 455 nm wavelengths. In both indices, the R2 between the estimated and the observed was as highas 0.94. © 2014 by the authors; licensee MDPI, Basel, Switzerland.

Ashourloo, D, Mobasheri, MR & Huete, A 2014, 'Evaluating the Effect of Different Wheat Rust Disease Symptoms on Vegetation Indices Using Hyperspectral Measurements', REMOTE SENSING, vol. 6, no. 6, pp. 5107-5123.
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© 2014 by the authors. Spectral Vegetation Indices (SVIs) have been widely used to indirectly detect plant diseases. The aim of this research is to evaluate the effect of different disease symptoms on SVIs and introduce suitable SVIs to detect rust disease. Wheat leaf rust is one of the prevalent diseases and has different symptoms including yellow, orange, dark brown, and dry areas. The reflectance spectrum data for healthy and infected leaves were collected using a spectroradiometer in the 450 to 1000 nm range. The ratio of the disease-affected area to the total leaf area and the proportion of each disease symptoms were obtained using RGB digital images. As the disease severity increases, so does the scattering of all SVI values. The indices were categorized into three groups based on their accuracies in disease detection. A few SVIs showed an accuracy of more than 60% in classification. In the first group, NBNDVI, NDVI, PRI, GI, and RVSI showed the highest amount of classification accuracy. The second and third groups showed classification accuracies of about 20% and 40% respectively. Results show that few indices have the ability to indirectly detect plant disease.

Ashrafinia, F, Mirmohammadali, M, Rajabi, H, Kazemnejad, A, SadeghniiatHaghighi, K, Amelvalizadeh, M & Chen, H 2014, 'The effects of Pilates exercise on sleep quality in postpartum women', Journal of Bodywork and Movement Therapies, vol. 18, no. 2, pp. 190-199.
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Prolonged poor sleeping quality can decrease women's ability to perform their maternal and family duties after delivery. The aim of this study was to investigate the effects of a Pilates training program on sleep quality in primigravida postpartum women in a randomized clinical trial. Eighty postpartum women were randomly divided into intervention and control groups (n=40). Home-based 30-min Pilate's exercises were started 72h after the delivery and performed five times per week for consecutive 8 weeks. Sleep quality was assessed by the Pittsburgh Sleep Quality Index (PSQI) prior to the intervention and 4th and 8th weeks afterwards. The intervention group showed a significant improvement in subjective sleep quality, sleep latency, daytime dysfunction and global PSQI score (P<0.001); however, there was no difference in sleep duration, habitual sleep efficiency and sleep disturbance between the groups. In conclusion, Pilates exercises appeared to improve sleep quality in primigravida postpartum women. © 2013 Elsevier Ltd.

Assaad, HI, Zhou, L, Carroll, RJ & Wu, G 2014, 'Rapid publication-ready MS-Word tables for one-way ANOVA', SpringerPlus, vol. 3, no. 1, pp. 1-8.
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© 2014, Assaad et al.; licensee Springer. Conclusions: Our new and user-friendly software to perform statistical analysis and generate publication-ready MS-Word tables for one-way ANOVA are expected to facilitate research in agriculture, biomedicine, and other fields of life sciences.Background: Statistical tables are an important component of data analysis and reports in biological sciences. However, the traditional manual processes for computation and presentation of statistically significant results using a letter-based algorithm are tedious and prone to errors.Results: Based on the R language, we present two web-based software for individual and summary data, freely available online, at http://shiny.stat.tamu.edu:3838/hassaad/Table_report1/ and http://shiny.stat.tamu.edu:3838/hassaad/SumAOV1/, respectively. The software are capable of rapidly generating publication-ready tables containing one-way analysis of variance (ANOVA) results. No download is required. Additionally, the software can perform multiple comparisons of means using the Duncan, Student-Newman-Keuls, Tukey Kramer, and Fisher’s least significant difference (LSD) tests. If the LSD test is selected, multiple methods (e.g., Bonferroni and Holm) are available for adjusting p-values. Using the software, the procedures of ANOVA can be completed within seconds using a web-browser, preferably Mozilla Firefox or Google Chrome, and a few mouse clicks. Furthermore, the software can handle one-way ANOVA for summary data (i.e. sample size, mean, and SD or SEM per treatment group) with post-hoc multiple comparisons among treatment means. To our awareness, none of the currently available commercial (e.g., SPSS and SAS) or open-source software (e.g., R and Python) can perform such a rapid task without advanced knowledge of the corresponding programming language.

Bachmann, NL, Fraser, TA, Bertelli, C, Jelocnik, M, Gillett, A, Funnell, O, Flanagan, C, Myers, GSA, Timms, P & Polkinghorne, A 2014, 'Comparative genomics of koala, cattle and sheep strains of Chlamydia pecorum', BMC Genomics, vol. 15, no. 1, pp. 1-14.
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BACKGROUND: Chlamydia pecorum is an important pathogen of domesticated livestock including sheep, cattle and pigs. This pathogen is also a key factor in the decline of the koala in Australia. We sequenced the genomes of three koala C. pecorum strains, isolated from the urogenital tracts and conjunctiva of diseased koalas. The genome of the C. pecorum VR629 (IPA) strain, isolated from a sheep with polyarthritis, was also sequenced. RESULTS: Comparisons of the draft C. pecorum genomes against the complete genomes of livestock C. pecorum isolates revealed that these strains have a conserved gene content and order, sharing a nucleotide sequence similarity > 98%. Single nucleotide polymorphisms (SNPs) appear to be key factors in understanding the adaptive process. Two regions of the chromosome were found to be accumulating a large number of SNPs within the koala strains. These regions include the Chlamydia plasticity zone, which contains two cytotoxin genes (toxA and toxB), and a 77 kbp region that codes for putative type III effector proteins. In one koala strain (MC/MarsBar), the toxB gene was truncated by a premature stop codon but is full-length in IPTaLE and DBDeUG. Another five pseudogenes were also identified, two unique to the urogenital strains C. pecorum MC/MarsBar and C. pecorum DBDeUG, respectively, while three were unique to the koala C. pecorum conjunctival isolate IPTaLE. An examination of the distribution of these pseudogenes in C. pecorum strains from a variety of koala populations, alongside a number of sheep and cattle C. pecorum positive samples from Australian livestock, confirmed the presence of four predicted pseudogenes in koala C. pecorum clinical samples. Consistent with our genomics analyses, none of these pseudogenes were observed in the livestock C. pecorum samples examined. Interestingly, three SNPs resulting in pseudogenes identified in the IPTaLE isolate were not found in any other C. pecorum strain analysed, raising questions over the ...

Baker, KE, Bonvini, SJ, Donovan, C, Foong, RE, Han, B, Jha, A, Shaifta, Y, Smit, M, Johnson, JR & Moir, LM 2014, 'Novel drug targets for asthma and COPD: Lessons learned from in vitro and in vivo models', PULMONARY PHARMACOLOGY & THERAPEUTICS, vol. 29, no. 2, pp. 181-198.
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Baldeaux, J, Ignatieva, K & Platen, E 2014, 'A tractable model for indices approximating the growth optimal portfolio', STUDIES IN NONLINEAR DYNAMICS AND ECONOMETRICS, vol. 18, no. 1, pp. 1-21.
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Ballerin, G, Ong, HX, Morgan, L, Oliver, B, Scalia, S, Young, PM & Traini, D 2014, 'THE EFFECTS OF SALBUTAMOL SULPHATE AND MANNITOL ON CILIARY BEAT FREQUENCY: A COMBINED THERAPY FOR MUCUS HYPER-SECRETION IN PULMONARY DISEASES', JOURNAL OF AEROSOL MEDICINE AND PULMONARY DRUG DELIVERY, vol. 27, no. 4, pp. A15-A16.

Banihashemi, N & Yalçın Kaya, C 2014, 'Inexact restoration and adaptive mesh refinement for optimal control', Journal of Industrial & Management Optimization, vol. 10, no. 2, pp. 521-542.
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Banville, N, Burgess, JK, Jaffar, J, Tjin, G, Richeldi, L, Cerri, S, Persiani, E, Black, JL & Oliver, BG 2014, 'A Quantitative Proteomic Approach to Identify Significantly Altered Protein Networks in the Serum of Patients with Lymphangioleiomyomatosis (LAM)', PLOS ONE, vol. 9, no. 8.
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Lymphangioleiomyomatosis (LAM) is a rare and progressive cystic lung condition affecting approximately 3.4-7.5/million women, with an average lag time between symptom onset and diagnosis of upwards of 4 years. The aim of this work was to identify altered proteins in LAM serum which may be potential biomarkers of disease. Serum from LAM patient volunteers and healthy control volunteers were pooled and analysis carried out using quantitative 4-plex iTRAQ technology. Differentially expressed proteins were validated using ELISAs and pathway analysis was carried out using Ingenuity Pathway Analysis. Fourteen proteins were differentially expressed in LAM serum compared to control serum (p<0.05). Further screening validated the observed differences in extracellular matrix remodelling proteins including fibronectin (30% decrease in LAM, p = 0.03), von Willebrand Factor (40% reduction in LAM, p = 0.03) and Kallikrein III (25% increase in LAM, p = 0.03). Pathway networks elucidated the relationships between the ECM and cell trafficking in LAM. This study was the first to highlight an imbalance in networks important for remodelling in LAM, providing a set of novel potential biomarkers. These understandings may lead to a new effective treatment for LAM in the future. © 2014 Banville et al.

Barnes, MK, Tilstone, GH, Smyth, TJ, Suggett, DJ, Astoreca, R, Lancelot, C & Kromkamp, JC 2014, 'Absorption-based algorithm of primary production for total and size-fractionated phytoplankton in coastal waters', Marine Ecology Progress Series, vol. 504, pp. 73-89.
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Most satellite models of production have been designed and calibrated for use in the open ocean. Coastal waters are optically more complex, and the use of chlorophyll a (chl a) as a first-order predictor of primary production may lead to substantial errors due to significant quantities of coloured dissolved organic matter (CDOM) and total suspended material (TSM) within the first optical depth. We demonstrate the use of phytoplankton absorption as a proxy to estimate primary production in the coastal waters of the North Sea and Western English Channel for both total, micro- and nano+pico-phytoplankton production. The method is implemented to extrapolate the absorption coefficient of phytoplankton and production at the sea surface to depth to give integrated fields of total and micro- and nano+pico-phytoplankton primary production using the peak in absorption coefficient at red wavelengths. The model is accurate to 8% in the Western English Channel and 22% in this region and the North Sea. By comparison, the accuracy of similar chl a based production models was >250%. The applicability of the method to autonomous optical sensors and remotely sensed aircraft data in both coastal and estuarine environments is discussed. © Inter-Research 2014.

Barnes, RJ, Bandi, RR, Chua, F, Low, JH, Aung, T, Barraud, N, Fane, AG, Kjelleberg, S & Rice, SA 2014, 'The roles of Pseudomonas aeruginosa extracellular polysaccharides in biofouling of reverse osmosis membranes and nitric oxide induced dispersal', JOURNAL OF MEMBRANE SCIENCE, vol. 466, pp. 161-172.
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Barraud, N, Kelso, M, Rice, S & Kjelleberg, S 2014, 'Nitric Oxide: A Key Mediator of Biofilm Dispersal with Applications in Infectious Diseases', Current Pharmaceutical Design, vol. 21, no. 1, pp. 31-42.
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Barraza, V, Grings, F, Ferrazzoli, P, Huete, A, Restrepo-Coupe, N, Beringer, J, Van Gorsel, E & Karszenbaum, H 2014, 'Behavior of multitemporal and multisensor passive microwave indices in Southern Hemisphere ecosystems', Journal of Geophysical Research-Biogeosciences, vol. 119, no. 12, pp. 2231-2244.
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©2014. American Geophysical Union. All Rights Reserved. This study focused on the time series analysis of passive microwave and optical satellite data collected from six Southern Hemisphere ecosystems in Australia and Argentina. The selected ecosystems represent a wide range of land cover types, including deciduous open forest, temperate forest, tropical and semiarid savannas, and grasslands. We used two microwave indices, the frequency index (FI) and polarization index (PI), to assess the relative contributions of soil and vegetation properties (moisture and structure) to the observations. Optical-based satellite vegetation products from the Moderate Resolution Imaging Spectroradiometer were also included to aid in the analysis. We studied the X and Ka bands of the Advanced Microwave Scanning Radiometer-EOS and Wind Satellite, resulting in up to four observations per day (1:30, 6:00, 13:30, and 18:00-h). Both the seasonal and hourly variations of each of the indices were examined. Environmental drivers (precipitation and temperature) and eddy covariance measurements (gross ecosystem productivity and latent energy) were also analyzed. It was found that in moderately dense forests, FI was dependent on canopy properties (leaf area index and vegetation moisture). In tropical woody savannas, a significant regression (R2) was found between FI and PI with precipitation (R2->-0.5) and soil moisture (R2->-0.6). In the areas of semiarid savanna and grassland ecosystems, FI variations found to be significantly related to soil moisture (R2->-0.7) and evapotranspiration (R2->-0.5), while PI varied with vegetation phenology. Significant differences (p-<-0.01) were found among FI values calculated at the four local times. Key Points Passive microwave indices can be used to estimate vegetation moisture Microwave observations were supported by flux data Passive microwave indices could be used to estimate evapotranspiration

Beck, HJ, Feary, DA, Figueira, WF & Booth, DJ 2014, 'Assessing range shifts of tropical reef fishes: a comparison of belt transect and roaming underwater visual census methods', BULLETIN OF MARINE SCIENCE, vol. 90, no. 2, pp. 705-721.
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Accurate, precise, and efficient underwater visual censuses (UVC) are vital for detecting and monitoring range shifts of reef fishes. The present study compared the utility of time-equivalent belt transects and Global Positioning System (GPS)-tracked roaming surveys for assessing populations of range-expanding tropical fishes off southeastern Australia. Roaming surveys were significantly more accurate and precise than belt transects in estimating densities of focal damselfish, Abudefduf vaigiensis (Quoy and Gaimard, 1825), while the accuracy and precision of density estimates did not significantly differ between methods for the rarer focal species, Abudefduf whitleyi (Allen and Robertson, 1974). Significantly greater species richness and assemblage diversity were detected by roaming surveys than belt transects. Roaming surveys were also over twice as efficient, defined as the area searched per unit time, as belt transects; mean efficiency of roaming surveys and belt transects was 33.56 (SE 1.22) and 12.57 (SE 0.66) m² min^-1, respectively. Results were consistent among observers with varied experience. Reliable density estimates, improved efficiency, and maximized sightings of tropical fishes suggest GPS-tracked roaming surveys are highly suited for detecting and monitoring range shifts of reef fishes.

Becker, EA, Seitzer, PM, Tritt, A, Larsen, D, Krusor, M, Yao, AI, Wu, D, Madern, D, Eisen, JA, Darling, AE & Facciotti, MT 2014, 'Phylogenetically Driven Sequencing of Extremely Halophilic Archaea Reveals Strategies for Static and Dynamic Osmo-response', PLoS Genetics, vol. 10, no. 11, pp. e1004784-e1004784.
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Bedon, F, Ziolkowski, L, Walford, SA, Dennis, ES & Llewellyn, DJ 2014, 'Members of the MYBMIXTA-like transcription factors may orchestrate the initiation of fiber development in cotton seeds', FRONTIERS IN PLANT SCIENCE, vol. 5.
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Behrendt, L, Nielsen, JL, Sorensen, SJ, Larkum, AWD, Winther, JR & Kuhl, M 2014, 'Rapid TaqMan-Based Quantification of Chlorophyll d-Containing Cyanobacteria in the Genus Acaryochloris', APPLIED AND ENVIRONMENTAL MICROBIOLOGY, vol. 80, no. 10, pp. 3244-3249.
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Reports of the chlorophyll (Chl) d-containing cyanobacterium Acaryochloris have accumulated since its initial discovery in 1996. The majority of this evidence is based on amplification of the gene coding for the 16S rRNA, and due to the wide geographical distribution of these sequences, a global distribution of Acaryochloris species was suggested. Here, we present a rapid, reliable, and cost-effective TaqMan-based quantitative PCR (qPCR) assay that was developed for the specific detection of Acaryochloris species in complex environmental samples. The TaqMan probe showed detection limits of ~10 16S rRNA gene copy numbers based on standard curves consisting of plasmid inserts. DNA from five Acaryochloris strains, i.e., MBIC11017, CCMEE5410, HICR111A, CRS, and Awaji-1, exhibited amplification efficiencies of >94% when tested in the TaqMan assay. When used on complex natural communities, the TaqMan assay detected the presence of Acaryochloris species in four out of eight samples of crustose coralline algae (CCA), collected from temperate and tropical regions. In three out of these TaqMan-positive samples, the presence of Chl d was confirmed via high-performance liquid chromatography (HPLC), and corresponding cell estimates of Acaryochloris species amounted to 7.6 × 101 to 3.0 × 103 per mg of CCA. These numbers indicate a substantial contribution of Chl d-containing cyanobacteria to primary productivity in endolithic niches. The new TaqMan assay allows quick and easy screening of environmental samples for the presence of Acaryochloris species and is an important tool to further resolve the global distribution and significance of this unique oxyphototroph.

Beitel, CW, Froenicke, L, Lang, JM, Korf, IF, Michelmore, RW, Eisen, JA & Darling, AE 2014, 'Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products', PeerJ, vol. 2, pp. e415-e415.
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Metagenomics is a valuable tool for the study of microbial communities but has been limited by the difficulty of binning the resulting sequences into groups corresponding to the individual species and strains that constitute the community. Moreover, there are presently no methods to track the flow of mobile DNA elements such as plasmids through communities or to determine which of these are co-localized within the same cell. We address these limitations by applying Hi-C, a technology originally designed for the study of three-dimensional genome structure in eukaryotes, to measure the cellular co-localization of DNA sequences. We leveraged Hi-C data generated from a simple synthetic metagenome sample to accurately cluster metagenome assembly contigs into groups that contain nearly complete genomes of each species. The Hi-C data also reliably associated plasmids with the chromosomes of their host and with each other. We further demonstrated that Hi-C data provides a long-range signal of strain-specific genotypes, indicating such data may be useful for high-resolution genotyping of microbial populations. Our work demonstrates that Hi-C sequencing data provide valuable information for metagenome analyses that are not currently obtainable by other methods. This metagenomic Hi-C method could facilitate future studies of the fine-scale population structure of microbes, as well as studies of how antibiotic resistance plasmids (or other genetic elements) mobilize in microbial communities. The method is not limited to microbiology; the genetic architecture of other heterogeneous populations of cells could also be studied with this technique.

Bellomo, R, Cass, A, Cole, L, Finfer, S, Gallagher, M, Lee, J, Lo, S, McArthur, C, McGuinness, S, Myburgh, J, Norton, R & Scheinkestel, C 2014, 'Calorie intake and patient outcomes in severe acute kidney injury: findings from The Randomized Evaluation of Normal vs. Augmented Level of Replacement Therapy (RENAL) study trial', Critical Care, vol. 18, no. 2, pp. R45-R45.
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Abstract Introduction Current practice in the delivery of caloric intake (DCI) in patients with severe acute kidney injury (AKI) receiving renal replacement therapy (RRT) is unknown. We aimed to describe calorie administration in patients enrolled in the Randomized Evaluation of Normal vs. Augmented Level of Replacement Therapy (RENAL) study and to assess the association between DCI and clinical outcomes. Methods We performed a secondary analysis in 1456 patients from the RENAL trial. We measured the dose and evolution of DCI during treatment and analyzed its association with major clinical outcomes using multivariable logistic regression, Cox proportional hazards models, and time adjusted models. Results Overall, mean DCI during treatment in ICU was low at only 10.9 ± 9 Kcal/kg/day for non-survivors and 11 ± 9 Kcal/kg/day for survivors. Among patients with a lower DCI (below the median) 334 of 729 (45.8%) had died at 90-days after randomization compared with 316 of 727 (43.3%) patients with a higher DCI (above the median) (P = 0.34). On multivariable logistic regression analysis, mean DCI carried an odds ratio of 0.95 (95% confidence interval (CI): 0.91-1.00; P = 0.06) per 100 Kcal increase for 90-day mortality. DCI was not associated with significant differences in renal replacement (RRT) free days, mechanical ventilation free days, ICU free days and hospital free days. These findings remained essentially unaltered after time adjusted analysis and Cox proportional hazards modeling. <...

Benedict, I, Corke, E, Morgan-Smith, R, Maynard, P, Curran, JM, Buckleton, J & Roux, C 2014, 'Geographical variation of shoeprint comparison class correspondences', Science & Justice, vol. 54, no. 5, pp. 335-337.
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The underlying principles involved in the interpretation of shoeprint comparisons have become a topical subject due to criticisms in the 2009 National Academy of Science (NAS) report on forensic sciences [1] . Difficulties in the application and understanding of these principles were also highlighted in a recent court ruling [25] and subsequent discussion of the ruling. We report here a survey that may inform some aspects of this interpretation and discuss the implications of findings from this survey in the light of that court ruling and more importantly the NAS report. 1,511 shoeprints were taken from student volunteers in Auckland, Wellington and Dunedin, New Zealand. 500 shoeprints were sampled from student volunteers at Australian universities. 100 from each of the University of Technology in Sydney, University of Queensland in Brisbane, University of Newcastle, Charles Sturt University in Bathurst and University of Canberra, Australia. These cities are distributed along the east coast of Australia. The shoeprints, taken from each country, were compared against each other for the presence of any pattern correspondences However shoeprints have not been compared between countries. In all locations the pattern of some common and many rare outsole patterns was repeated, with Converse Chuck Taylor All Stars and Vans Canvas Era common in all locations.

Bengtson Nash, S, Dawson, A, Burkhard, M, Waugh, C & Huston, W 2014, 'Detoxification enzyme activities (CYP1A1 and GST) in the skin of humpback whales as a function of organochlorine burdens and migration status', Aquatic Toxicology, vol. 155, pp. 207-212.
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The activities of glutathione-s-transferase (GST) and cytochrome P-450 1A1 (CYP1A1) enzymes were measured in freshly extracted epidermis of live-biopsied, migrating, southern hemisphere humpback whales (Megaptera novaeangliae). The two quantified enzyme activities did not correlate strongly with each other. Similarly, neither correlated strongly with any of the organochlorine compound groups previously measured in the superficial blubber of the sample biopsy core, likely reflecting the anticipated low levels of typical aryl-hydrocarbon receptor ligands. GST activity did not differ significantly between genders or between northward (early migration) or southward (late migration) migrating cohorts. Indeed, the inter-individual variability in GST measurements was relatively low. This observation raises the possibility that measured activities were basal activities and that GST function was inherently impacted by the fasting state of the sampled animals, as seen in other species. These results do not support the implementation of CYP1A1 or GST as effective biomarkers of organochlorine contaminant burdens in southern hemisphere populations of humpback whales as advocated for other cetacean species. Further investigation of GST activity in feeding versus fasting cohorts may, however, provide some insight into the fasting metabolism of these behaviourally adapted populations.

Ben-Nissan, B 2014, 'Biomimetics and Marine Materials in Drug Delivery and Tissue Engineering: From Natural Role Models to Bone Regeneration', Key Engineering Materials, vol. 587, pp. 229-232.
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During the last two decades learning from nature has given us new directions for the use of natural organic and inorganic skeletons, drug delivery devices, new medical treatment methods initiating unique designs and devices ranging from nanoto macro scale. These materials and designs have been instrumental to introduce the simplest remedies to vital problems in regenerative medicine, providing frameworks and highly accessible sources of osteopromotive analogues, naofibres, micro and macrospheres and mineralising proteins. This is exemplified by the biological effectiveness of marine structures such as corals and shells and sponge skeletons to house self-sustaining musculoskeletal tissues and to the promotion of bone formation by extracts of spongin and nacre seashells. Molecules pivotal to the regulation and guidance of bone morphogenesis and particularly the events in mineral metabolism and deposition similarly exist in the earliest marine organisms because they represent the first molecular components established for calcification, morphogenesis and wound healing. It emerges that bone morphogenic protein (BMP) molecules-the main cluster of bone growth factors for human bone morphogenesis-are secreted by endodermal cells into the developing skeleton. Signalling proteins, TGF and Wnt-prime targets in bone therapeutics-are present in early marine sponge development. Furthermore, ready-made organic and inorganic marine skeletons possess a habitat suitable for proliferating added mesenchymal stem cell populations and promoting clinically acceptable bone formation. In this paper we review the nature, morphology and extent of this association and use of these structures for bone grafts, drug delivery and extracts such as proteins for regenerative medicine. As an example, in human biology a study of matrix vesicles will teach us valuable lessons on how proteins are captured and coated; and how the vesicle is able to dock and fuse with their target. We...

Blackman, CJ, Gleason, SM, Chang, Y, Cook, AM, Laws, C & Westoby, M 2014, 'Leaf hydraulic vulnerability to drought is linked to site water availability across a broad range of species and climates', Annals of Botany, vol. 114, no. 3, pp. 435-440.
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Boakes, RA, Rooney, KB & Kendig, MD 2014, 'Sugar-sweetened drinks for rats. Bad for their bodies and bad for their brains', Appetite, vol. 83, pp. 342-342.
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Boakes, RA, Rooney, KB, Kendig, MD & Martire, SI 2014, 'Access to glucose-sweetened yoghurt or solution produces enlarged fat pads in the rat', Obesity Research & Clinical Practice, vol. 8, pp. 9-9.
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Booth, DJ 2014, 'Do otolith increments allow correct inferences about age and growth of coral reef fishes?', CORAL REEFS, vol. 33, no. 1, pp. 255-258.
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Otolith increment structure is widely used to estimate age and growth of marine fishes. Here, I test the accuracy of the long-term otolith increment analysis of the lemon damselfish Pomacentrus moluccensis to describe age and growth characteristics. I compare the number of putative annual otolith increments (as a proxy for actual age) and widths of these increments (as proxies for somatic growth) with actual tagged fish-length data, based on a 6-year dataset, the longest time course for a coral reef fish. Estimated age from otoliths corresponded closely with actual age in all cases, confirming annual increment formation. However, otolith increment widths were poor proxies for actual growth in length [linear regression r 2 = 0.44-0.90, n = 6 fish] and were clearly of limited value in estimating annual growth. Up to 60 % of the annual growth variation was missed using otolith increments, suggesting the long-term back calculations of otolith growth characteristics of reef fish populations should be interpreted with caution. © 2013 Springer-Verlag Berlin Heidelberg.

Booth, DJ, Poulos, DE, Poole, J & Feary, DA 2014, 'Growth and temperature relationships for juvenile fish species in seagrass beds: implications of climate change', JOURNAL OF FISH BIOLOGY, vol. 84, no. 1, pp. 231-236.
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The effect of water temperature on growth responses of three common seagrass fish species that co-occur as juveniles in the estuaries in Sydney (34° S) but have differing latitudinal ranges was measured: Pelates sexlineatus (subtropical to warm temperate: 27-35° S), Centropogon australis (primarily subtropical to warm temperate: 24-37° S) and Acanthaluteres spilomelanurus (warm to cool temperate: below 32° S). Replicate individuals of each species were acclimated over a 7day period in one of three temperature treatments (control: 22°C, low: 18°C and high: 26°C) and their somatic growth was assessed within treatments over 10days. Growth of all three species was affected by water temperature, with the highest growth of both northern species (P. sexlineatus and C. australis) at 22 and 26°C, whereas growth of the southern ranging species (A. spilomelanurus) was reduced at temperatures higher than 18°C, suggesting that predicted increase in estuarine water temperatures through climate change may change relative performance of seagrass fish assemblages. © 2013 The Fisheries Society of the British Isles.

Bottomley, AL, Kabli, AF, Hurd, AF, Turner, RD, Garcia-Lara, J & Foster, SJ 2014, 'Staphylococcus aureus DivIB is a peptidoglycan-binding protein that is required for a morphological checkpoint in cell division', MOLECULAR MICROBIOLOGY, vol. 94, no. 5, pp. 1041-1064.
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© 2014 The Authors. Molecular Microbiology published by John Wiley & Sons Ltd. Bacterial cell division is a fundamental process that requires the coordinated actions of a number of proteins which form a complex macromolecular machine known as the divisome. The membrane-spanning proteins DivIB and its orthologue FtsQ are crucial divisome components in Gram-positive and Gram-negative bacteria respectively. However, the role of almost all of the integral division proteins, including DivIB, still remains largely unknown. Here we show that the extracellular domain of DivIB is able to bind peptidoglycan and have mapped the binding to its β subdomain. Conditional mutational studies show that divIB is essential for Staphylococcus aureus growth, while phenotypic analyses following depletion of DivIB results in a block in the completion, but not initiation, of septum formation. Localisation studies suggest that DivIB only transiently localises to the division site and may mark previous sites of septation. We propose that DivIB is required for a molecular checkpoint during division to ensure the correct assembly of the divisome at midcell and to prevent hydrolytic growth of the cell in the absence of a completed septum.

Bourke, JE, Bai, Y, Donovan, C, Esposito, JG, Tan, X & Sanderson, MJ 2014, 'Novel Small Airway Bronchodilator Responses to Rosiglitazone in Mouse Lung Slices', American Journal of Respiratory Cell and Molecular Biology, vol. 50, no. 4, pp. 748-756.
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There is a need to identify novel agents that elicit small airway relaxation when β2-adrenoceptor agonists become ineffective in difficult-to-treat asthma. Because chronic treatment with the synthetic peroxisome proliferator activated receptor (PPAR)γ agonist rosiglitazone (RGZ) inhibits airway hyperresponsiveness in mouse models of allergic airways disease, we tested the hypothesis that RGZ causes acute airway relaxation by measuring changes in small airway size in mouse lung slices. Whereas the β-adrenoceptor agonists albuterol (ALB) and isoproterenol induced partial airway relaxation, RGZ reversed submaximal and maximal contraction to methacholine (MCh) and was similarly effective after precontraction with serotonin or endothelin-1. Concentration-dependent relaxation to RGZ was not altered by the β-adrenoceptor antagonist propranolol and was enhanced by ALB. RGZ-induced relaxation wasmimicked by other synthetic PPARγ agonists but not by the putative endogenous agonist 15-deoxy-PGJ2 and was not prevented by the PPARγ antagonist GW9662. To induce airway relaxation, RGZ inhibited the amplitude and frequency of MCh-induced Ca2+ oscillations of airway smooth muscle cells (ASMCs). In addition, RGZ reduced MCh-induced Ca2+ sensitivity of the ASMCs. Collectively, these findings demonstrate that acute bronchodilator responses induced by RGZ are PPARγ independent, additive with ALB, and occur by the inhibition of ASMC Ca2+ signaling and Ca2+ sensitivity. Because RGZ continues to elicit relaxation when β-adrenoceptor agonists have a limited effect, RGZ or related compounds may have potential as bronchodilators for the treatment of difficult asthma. Copyright © 2014 by the American Thoracic Society.

Brito, B, Dee, S, Wayne, S, Alvarez, J & Perez, A 2014, 'Genetic Diversity of PRRS Virus Collected from Air Samples in Four Different Regions of Concentrated Swine Production during a High Incidence Season', Viruses, vol. 6, no. 11, pp. 4424-4436.
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Porcine Reproductive and Respiratory Syndrome (PRRS) is one of the most relevant swine diseases in the US, costing the industry millions of dollars per year. Unfortunately, disease control is difficult because of the virus dynamics, as PRRS virus (PRRSV) can be transmitted by air between farms, especially, in regions with high density of swine operations. While long distance airborne transport of PRRSV has been reported, there is little information regarding the dynamics of PRRSV airborne challenge in concentrated regions. The objective of this study was to describe the frequency of detection, dose and diversity of PRRSV in air samples collected across four concentrated production regions during the PRRS-high risk season in the Midwestern US (October–December) in 2012. Between 29% and 42% of the air samples were positive in all four sampling sites. Sequencing of the recovered virus showed a wide diversity of field and vaccine variants. Higher frequency, dose, and diversity of PRRSV were observed in air at locations with higher pig density. These findings suggest that regional spread of PRRSV due to aerosol transmission of PRRSV represents a significant risk to susceptible herds in concentrated regions of domestic pig production where PRRSV is endemic.

Brito, BP, Aly, SS, Anderson, RJ, Fossler, CP, Garry, FB & Gardner, IA 2014, 'Association between caudal fold tuberculin test responses and results of an ELISA for Mycobacterium avium subsp paratuberculosis and mycobacterial culture of feces in tuberculosis-free dairy herds', Journal of the American Veterinary Medical Association, vol. 244, no. 5, pp. 582-587.
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AbstractObjective—To evaluate associations between Mycobacterium avium subsp paratuberculosis (MAP) and caudal fold tuberculin (CFT) test results in cattle.Design—Longitudinal and cross-sectional evaluations.Animals—1 California (approx 3,600 cows) and 3 Colorado (approx 640, 1,190, and 1,480 cows) dairy herds considered free of Mycobacterium bovis infection.Procedures—In the California herd, the association between CFT response and MAP status was determined with ELISA and mycobacterial culture of feces within 1 year before and after CFT testing. The association between CFT and MAP status in all herds was modeled with mixed-effects logistic regression.Results—In the California herd, significantly higher odds of being classified as suspect by CFT were found for cows with results of MAP ELISA negative before and positive after CFT testing (OR, 5.6) and cows positive before and after CFT testing (OR, 8.1). Higher odds were found for cows positive for mycobacterial culture of feces before and negative for culture after CFT testing (OR, 4.6) and cows negative for mycobacterial culture of feces before and positive for culture after CFT testing (OR, 13.2). All herds had higher odds of being classified as suspect by CFT testing for cows with positive results for ELISA (OR, 2.9) or mycobacterial culture of feces (OR, 5.0), compared with cows with negative results of the same tests.Conclusions and Clinical Relevance—A strong association was found between positive MAP test results and being classified as a suspect by CFT testing. Within-herd MAP prevalence may affect specificity of CFT testing for tuberculosis in cattle.

Brito, BP, Perez, AM & Capozzo, AV 2014, 'Accuracy of traditional and novel serology tests for predicting cross-protection in foot-and-mouth disease vaccinated cattle', Vaccine, vol. 32, no. 4, pp. 433-436.
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Brodersen, KE, Nielsen, DA, Ralph, PJ & Kuhl, M 2014, 'A split flow chamber with artificial sediment to examine the below-ground microenvironment of aquatic macrophytes', MARINE BIOLOGY, vol. 161, no. 12, pp. 2921-2930.
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Brodie, J, Williamson, CJ, Smale, DA, Kamenos, NA, Mieszkowska, N, Santos, R, Cunliffe, M, Steinke, M, Yesson, C, Anderson, KM, Asnaghi, V, Brownlee, C, Burdett, HL, Burrows, MT, Collins, S, Donohue, PJC, Harvey, B, Foggo, A, Noisette, F, Nunes, J, Ragazzola, F, Raven, JA, Schmidt, DN, Suggett, D, Teichberg, M & Hall‐Spencer, JM 2014, 'The future of the northeast Atlantic benthic flora in a high CO₂ world', Ecology and Evolution, vol. 4, no. 13, pp. 2787-2798.
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AbstractSeaweed and seagrass communities in the northeast Atlantic have been profoundly impacted by humans, and the rate of change is accelerating rapidly due to runaway CO2 emissions and mounting pressures on coastlines associated with human population growth and increased consumption of finite resources. Here, we predict how rapid warming and acidification are likely to affect benthic flora and coastal ecosystems of the northeast Atlantic in this century, based on global evidence from the literature as interpreted by the collective knowledge of the authorship. We predict that warming will kill off kelp forests in the south and that ocean acidification will remove maerl habitat in the north. Seagrasses will proliferate, and associated epiphytes switch from calcified algae to diatoms and filamentous species. Invasive species will thrive in niches liberated by loss of native species and spread via exponential development of artificial marine structures. Combined impacts of seawater warming, ocean acidification, and increased storminess may replace structurally diverse seaweed canopies, with associated calcified and noncalcified flora, with simple habitats dominated by noncalcified, turf‐forming seaweeds.

Broich, M, Huete, A, Tulbure, MG, Ma, X, Xin, Q, Paget, M, Restrepo-Coupe, N, Davies, K, Devadas, R & Held, A 2014, 'Land surface phenological response to decadal climate variability across Australia using satellite remote sensing', Biogeosciences Discussions, vol. 11, no. 5, pp. 7685-7719.
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Abstract. Land surface phenological cycles of vegetation greening and browning are influenced by variability in climatic forcing. Quantitative information on phenological cycles and their variability is important for agricultural applications, wildfire fuel accumulation, land management, land surface modeling, and climate change studies. Most phenology studies have focused on temperature-driven Northern Hemisphere systems, where phenology shows annually reoccurring patterns. Yet, precipitation-driven non-annual phenology of arid and semi-arid systems (i.e. drylands) received much less attention, despite the fact that they cover more than 30% of the global land surface. Here we focused on Australia, the driest inhabited continent with one of the most variable rainfall climates in the world and vast areas of dryland systems. Detailed and internally consistent studies investigating phenological cycles and their response to climate variability across the entire continent designed specifically for Australian dryland conditions are missing. To fill this knowledge gap and to advance phenological research, we used existing methods more effectively to study geographic and climate-driven variability in phenology over Australia. We linked derived phenological metrics with rainfall and the Southern Oscillation Index (SOI). We based our analysis on Enhanced Vegetation Index (EVI) data from the MODerate Resolution Imaging Spectroradiometer (MODIS) from 2000 to 2013, which included extreme drought and wet years. We conducted a continent-wide investigation of the link between phenology and climate variability and a more detailed investigation over the Murray–Darling Basin (MDB), the primary agricultural area and largest river catchment of Australia. Results showed high inter- and intra-annual variability in phenological cycles. Phenological cycle peaks occurred not only during the austral summer but at any time of the year, and their timing varied by more than ...

Brown, BE, Kim, CHJ, Torpy, FR, Bursill, CA, McRobb, LS, Heather, AK, Davies, MJ & van Reyk, DM 2014, 'Supplementation with carnosine decreases plasma triglycerides and modulates atherosclerotic plaque composition in diabetic apo E-/- mice', ATHEROSCLEROSIS, vol. 232, no. 2, pp. 403-409.
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Objective: Carnosine has been shown to modulate triglyceride and glycation levels in cell and animal systems. In this study we investigated whether prolonged supplementation with carnosine inhibits atherosclerosis and markers of lesion stability in hyperglycaemic and hyperlipidaemic mice. Methods: Streptozotocin-induced diabetic apo E-/- mice were maintained for 20 weeks, post-induction of diabetes. Half of the animals received carnosine (2g/L) in their drinking water. Diabetes was confirmed by significant increases in blood glucose and glycated haemoglobin, plasma triglyceride and total cholesterol levels, brachiocephalic artery and aortic sinus plaque area; and lower body mass. Results: Prolonged carnosine supplementation resulted in a significant (~20-fold) increase in plasma carnosine levels, and a significant (~23%) lowering of triglyceride levels in the carnosine-supplemented groups regardless of glycaemic status. Supplementation did not affect glycaemic status, blood cholesterol levels or loss of body mass. In the diabetic mice, carnosine supplementation did not diminish measured plaque area, but reduced the area of plaque occupied by extracellular lipid (~60%) and increased both macrophage numbers (~70%) and plaque collagen content (~50%). The area occupied by α-actin-positive smooth muscle cells was not significantly increased. Conclusions: These data indicate that in a well-established model of diabetes-associated atherosclerosis, prolonged carnosine supplementation enhances plasma levels, and has novel and significant effects on atherosclerotic lesion lipid, collagen and macrophage levels. These data are consistent with greater lesion stability, a key goal in treatment of existing cardiovascular disease. Carnosine supplementation may therefore be of benefit in lowering triglyceride levels and suppressing plaque instability in diabetes-associated atherosclerosis. © 2013 Elsevier Ireland Ltd.

Buettner, TFS, Kabakova, IV, Hudson, DD, Pant, R, Poulton, CG, Judge, AC & Eggleton, BJ 2014, 'Phase-locking in Multi-Frequency Brillouin Oscillator via Four Wave Mixing', Scientific Reports, vol. 4.
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Stimulated Brillouin scattering (SBS) and Kerr-nonlinear four wave-mixing(FWM) are among the most important and widely studied nonlinear effects inoptical fibres. At high powers SBS can be cascaded producing multiple Stokeswaves spaced by the Brillouin frequency shift. Here, we investigate the complexnonlinear interaction of the cascade of Stokes waves, generated in aFabry-Perot chalcogenide fibre resonator through the combined action of SBS andFWM. We demonstrate the existence of parameter regimes, in which pump andStokes waves attain a phase-locked steady state. Real-time measurements of 40pspulses with 8GHz repetition rate are presented, confirming short-and long-termstability. Numerical simulations qualitatively agree with experiments and showthe significance of FWM in phase-locking of pump and Stokes waves. Our findingscan be applied for the design of novel picosecond pulse sources with GHzrepetition rate for optical communication systems.

Burillo, J & Elder, M 2014, 'Metric properties of Baumslag-Solitar groups', International Journal of Algebra and Computation, vol. 25, pp. 799-811.
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We compute estimates for the word metric of Baumslag--Solitar groups in termsof the Britton's lemma normal form. As a corollary, we find lower bounds forthe growth rate for the groups $BS(p,q)$, with $1

Burton, BA, Elder, M, Kalka, A & Tillmann, S 2014, '2-manifold recognition is in logspace', Journal of Computational Geometry, vol. 7, pp. 70-85.
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We prove that the homeomorphism problem for 2-manifolds can be decided inlogspace. The proof relies on Reingold's logspace solution to the undirected$s,t$-connectivity problem in graphs.

Busschaert, N, Karagiannidis, LE, Wenzel, M, Haynes, CJE, Wells, NJ, Young, PG, Makuc, D, Plavec, J, Jolliffe, KA & Gale, PA 2014, 'Synthetic transporters for sulfate: a new method for the direct detection of lipid bilayer sulfate transport', Chemical Science, vol. 5, no. 3, pp. 1118-1118.
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Butt, FK, Tahir, M, Cao, C, Idrees, F, Ahmed, R, Khan, WS, Ali, Z, Mahmood, N, Tanveer, M, Mahmood, A & Aslam, I 2014, 'Synthesis of Novel ZnV₂O₄ Hierarchical Nanospheres and Their Applications as Electrochemical Supercapacitor and Hydrogen Storage Material', ACS Applied Materials & Interfaces, vol. 6, no. 16, pp. 13635-13641.
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Büttner, TFS, Merklein, M, Kabakova, IV, Hudson, DD, Choi, D-Y, Luther-Davies, B, Madden, SJ & Eggleton, BJ 2014, 'Phase-locked, chip-based, cascaded stimulated Brillouin scattering', Optica, vol. 1, no. 5, pp. 311-311.
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Callsen, G, Wagner, MR, Reparaz, JS, Nippert, F, Kure, T, Kalinowski, S, Hoffmann, A, Ford, MJ, Phillips, MR, Dalmau, RF, Schlesser, R, Collazo, R & Sitar, Z 2014, 'Phonon pressure coefficients and deformation potentials of wurtzite AlN determined by uniaxial pressure-dependent Raman measurements', PHYSICAL REVIEW B, vol. 90, no. 20.
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© 2014 American Physical Society. We studied bulk crystals of wurtzite AlN by means of uniaxial pressure-dependent Raman measurements. As a result, we derive the phonon pressure coefficients and deformation potentials for all zone center optical phonon modes. For the A1 and E1 modes, we further experimentally determined the uniaxial pressure dependence of their longitudinal optical-transverse optical (LO-TO) splittings. Our experimental approach delivers new insight into the large variance among previously reported phonon deformation potentials, which are predominantly based on heteroepitaxial growth of AlN and the ball-on-ring technique. Additionally, the measured phonon pressure coefficients are compared to their theoretical counterparts obtained by density functional theory implemented in the siesta package. Generally, we observe a good agreement between the calculated and measured phonon pressure coefficients but some particular Raman modes exhibit significant discrepancies similar to the case of wurtzite GaN and ZnO, clearly motivating the presented uniaxial pressure-dependent Raman measurements on bulk AlN crystals.

Canning, J, Huyang, G, Ma, M, Beavis, A, Bishop, D, Cook, K, McDonagh, A, Shi, D, Peng, G-D & Crossley, MJ 2014, 'Percolation Diffusion into Self-Assembled Mesoporous Silica Microfibres', NANOMATERIALS, vol. 4, no. 1, pp. 157-174.
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Percolation diffusion into long (11.5 cm) self-assembled, ordered mesoporous microfibres is studied using optical transmission and laser ablation inductive coupled mass spectrometry (LA-ICP-MS). Optical transmission based diffusion studies reveal rapid penetration (< 5 s, D > 80 um2.s-1) of Rhodamine B with very little percolation of larger molecules such as zinc tetraphenylporphyrin (ZnTPP) observed under similar loading conditions. The failure of ZnTPP to enter the microfibre was confirmed, in higher resolution, using LA-ICP-MS. In the latter case, LA-ICP-MS was used to determine the diffusion of zinc acetate dihydrate, D ~ 3 x 10-4 nm2.s-1. The large differences between the molecules are accounted for by proposing ordered solvent and structure assisted accelerated diffusion of the Rhodamine B based on its hydrophilicity relative to the zinc compounds. The broader implications and applications for filtration, molecular sieves and a range of devices and uses are described.

Cao, X, Chen, S & Wang, G 2014, 'Porous carbon particles derived from natural peanut shells as lithium ion battery anode and its electrochemical properties', Electronic Materials Letters, vol. 10, no. 4, pp. 819-826.
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Care, A, Chi, F, Bergquist, PL & Sunna, A 2014, 'Biofunctionalization of silica-coated magnetic particles mediated by a peptide', Journal of Nanoparticle Research, vol. 16, no. 8.
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Care, A, Nevalainen, H, Bergquist, PL & Sunna, A 2014, 'Effect of Trichoderma reesei Proteinases on the Affinity of an Inorganic-Binding Peptide', Applied Biochemistry and Biotechnology, vol. 173, no. 8, pp. 2225-2240.
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Carroll, RJ, Page, RD, Joss, DT, Uusitalo, J, Darby, IG, Andgren, K, Cederwall, B, Eeckhaudt, S, Grahn, T, Gray-Jones, C, Greenlees, PT, Hadinia, B, Jones, PM, Julin, R, Juutinen, S, Leino, M, Leppänen, A-P, Nyman, M, O’Donnell, D, Pakarinen, J, Rahkila, P, Sandzelius, M, Sarén, J, Scholey, C, Seweryniak, D & Simpson, J 2014, 'Blurring the Boundaries: Decays of Multiparticle Isomers at the Proton Drip Line', Physical Review Letters, vol. 112, no. 9.
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A multiparticle spin-trap isomer has been discovered in the proton-unbound nucleus Ta85 73158. The isomer mainly decays by γ-ray emission with a half-life of 6.1(1) μs. Analysis of the γ-ray data shows that the isomer lies 2668 keV above the known 9+ state and has a spin 10 higher and negative parity. This 19- isomer also has an 8644(11) keV, 1.4(2)% α-decay branch that populates the 9+ state in Lu154. No proton-decay branch from the isomer was identified, despite the isomer being unbound to proton emission by 3261(14) keV. This remarkable stability against proton emission is compared with theoretical predictions, and the implications for the extent of observable nuclides are considered. © 2014 American Physical Society.

Castelletto, S, Bodrog, Z, Magyar, AP, Gentle, A, Gali, A & Aharonovich, I 2014, 'Quantum-confined single photon emission at room temperature from SiC tetrapods', NANOSCALE, vol. 6, no. 17, pp. 10027-10032.
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Controlled engineering of isolated solid state quantum systems is one of the most prominent goals in modern nanotechnology. In this letter we demonstrate a previously unknown quantum system namely silicon carbide tetrapods. The tetrapods have a cubic polytype core (3C) and hexagonal polytype legs (4H)-a geometry that creates spontaneous polarization within a single tetrapod. Modeling of the tetrapod structures predicts that a bound exciton should exist at the 3C-4H interface. The simulations are confirmed by the observation of fully polarized and narrowband single photon emission from the tetrapods at room temperature. The single photon emission provides important insights into understanding the quantum confinement effects in non-spherical nanostructures. Our results pave the way to a new class of crystal phase nanomaterials that exhibit single photon emission at room temperature and therefore are suitable for sensing, quantum information and nanophotonics. © 2014 the Partner Organisations.

Castelletto, S, Johnson, BC, Zachreson, C, Beke, D, Balogh, I, Ohshima, T, Aharonovich, I & Gali, A 2014, 'Room Temperature Quantum Emission from Cubic Silicon Carbide Nanoparticles', ACS NANO, vol. 8, no. 8, pp. 7938-7947.
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The photoluminescence (PL) arising from silicon carbide nanoparticles has so far been associated with the quantum confinement effect or to radiative transitions between electronically active surface states. In this work we show that cubic phase silicon carbide nanoparticles with diameters in the range 45-500 nm can host other point defects responsible for photoinduced intrabandgap PL. We demonstrate that these nanoparticles exhibit single photon emission at room temperature with record saturation count rates of 7 × 106 counts/s. The realization of nonclassical emission from SiC nanoparticles extends their potential use from fluorescence biomarker beads to optically active quantum elements for next generation quantum sensing and nanophotonics. The single photon emission is related to single isolated SiC defects that give rise to states within the bandgap. © 2014 American Chemical Society.

Castorina, A & Giunta, S 2014, 'Mucin 1 (MUC1) signalling contributes to increase the resistance to cell death in human bronchial epithelial cells exposed to nickel acetate', BioMetals, vol. 27, no. 6, pp. 1149-1158.
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Castorina, A, Scuderi, S, D’Amico, AG, Drago, F & D’Agata, V 2014, 'PACAP and VIP increase the expression of myelin-related proteins in rat schwannoma cells: Involvement of PAC1/VPAC2 receptor-mediated activation of PI3K/Akt signaling pathways', Experimental Cell Research, vol. 322, no. 1, pp. 108-121.
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Cavaliere, R, Ball, JL, Turnbull, L & Whitchurch, CB 2014, 'The biofilm matrix destabilizers, EDTA and DNaseI, enhance the susceptibility of nontypeable Hemophilus influenzae biofilms to treatment with ampicillin and ciprofloxacin', MICROBIOLOGYOPEN, vol. 3, no. 4, pp. 557-567.
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Nontypeable Hemophilus influenzae (NTHi) is a Gram-negative bacterial pathogen that causes chronic biofilm infections of the ears and airways. The biofilm matrix provides structural integrity to the biofilm and protects biofilm cells from antibiotic exposure by reducing penetration of antimicrobial compounds into the biofilm. Extracellular DNA (eDNA) has been found to be a major matrix component of biofilms formed by many species of Gram-positive and Gram-negative bacteria, including NTHi. Interestingly, the cation chelator ethylenediaminetetra-acetic acid (EDTA) has been shown to reduce the matrix strength of biofilms of several bacterial species as well as to have bactericidal activity against various pathogens. EDTA exerts its antimicrobial activity by chelating divalent cations necessary for growth and membrane stability and by destabilizing the matrix thus enhancing the detachment of bacterial cells from the biofilm. In this study, we have explored the role of divalent cations in NTHi biofilm development and stability. We have utilized in vitro static and continuous flow models of biofilm development by NTHi to demonstrate that magnesium cations enhance biofilm formation by NTHi. We found that the divalent cation chelator EDTA is effective at both preventing NTHi biofilm formation and at treating established NTHi biofilms. Furthermore, we found that the matrix destablilizers EDTA and DNaseI increase the susceptibility of NTHi biofilms to ampicillin and ciprofloxacin. Our observations indicate that DNaseI and EDTA enhance the efficacy of antibiotic treatment of NTHi biofilms. These observations may lead to new strategies that will improve the treatment options available to patients with chronic NTHi infections. © 2014 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Chacko, A, Barker, CJ, Beagley, KW, Hodson, MP, Plan, MR, Timms, P & Huston, WM 2014, 'Increased sensitivity to tryptophan bioavailability is a positive adaptation by the human strains of Chlamydia pneumoniae', Molecular Microbiology, vol. 93, no. 4, pp. 797-813.
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SummaryOne of the most significant activities induced by interferon‐gamma against intracellular pathogens is the induction of IDO (indoleamine 2,3‐dioxygenase) expression, which subsequently results in the depletion of tryptophan. We tested the hypothesis that human strains of Chlamydia pneumoniae are more sensitive to tryptophan limitation than animal C. pneumoniae strains. The human strains were significantly more sensitive to IFN‐γ than the animal strains in a lung epithelia cell model (BEAS‐2B), with exposure to 1 U ml−1 IFN‐γ resulting in complete loss of infectious yield of human strains, compared to the animal strains where reductions in infectious progeny were around 3.5–4.0 log. Strikingly, the IFN‐γ induced loss of ability to form infectious progeny production was completely rescued by removal of the IFN‐γ and addition of exogenous tryptophan for the human strains, but not the animal strains. In fact, a human heart strain was more capable of entering a non‐infectious, viable persistent stage when exposed to IFN‐γ and was also more effectively rescued, compared to a human respiratory strain. Exquisite susceptibility to IFN

Chadwick, S, Xiao, L, Maynard, P, Lennard, C, Spindler, X & Roux, C 2014, 'PolyCyano UV: an investigation into a one-step luminescent cyanoacrylate fuming process', AUSTRALIAN JOURNAL OF FORENSIC SCIENCES, vol. 46, no. 4, pp. 471-484.
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© 2014 Australian Academy of Forensic Sciences. PolyCyano UV (Foster + Freeman Ltd) is a new one-step process for developing luminescent fingermarks using cyanoacrylate (CA) fuming without the need for further chemical treatment. In this study, conditions including the amount of PolyCyano UV powder, the humidity level of the fuming chamber, and the time and temperature of the fuming process were optimised. A variety of different surfaces were tested and aged fingermark samples were also examined. The PolyCyano-UV-developed fingermarks were compared with conventional CA-developed fingermarks and subsequently stained with rhodamine 6G. PolyCyano UV was able to develop high-quality fingermarks on the surfaces tested. However, when examined under UV light, the luminescence of PolyCyano-UV-developed fingermarks was found to be weaker than conventional CA-developed fingermarks that were stained with rhodamine 6G. When used in sequence with rhodamine 6G, PolyCyano UV was found to give significantly improved contrast compared with conventional CA-developed fingermarks stained with rhodamine 6G.

Chambers, DC, Gellatly, SL, Hugenholtz, P & Hansbro, PM 2014, 'JTD special edition 'Hot Topics in COPD'-The microbiome in COPD.', J Thorac Dis, vol. 6, no. 11, pp. 1525-1531.
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The pathogenesis of chronic obstructive pulmonary disease (COPD) and its exacerbations, are intricately linked to colonisation and infection with bacteria and other microbes. Despite their undeniable importance, we have a poor understanding of the complex relationships between COPD phenotypes, physiology, cellular and molecular biology and the roles of colonising microbe or infecting pathogens. The management algorithms for the care of patients with COPD that include microbial influences, have almost exclusively been developed using microbial methods that were entirely dependent on the ability to grow bacteria on suitable media. The shortcomings of this approach are becoming clear now that it is possible to completely and accurately define the microbial ecology of ecosystems using genomic methods, which do not rely on the ability to cultivate the organisms present. Whilst our appreciation of the relationships between some bacterial ecosystems and the organ in which they reside in humans is now relatively advanced, this is not true for lung. This perspective serves to highlight the growing importance of including an accurate description of bacterial ecology in any attempt to decipher the pathobiology of COPD. While this field is in its infancy, there is significant potential to gain new insights which will translate into more rational and effective treatment algorithms for patients with COPD.

Chan, JGY, Tyne, AS, Pang, A, Chan, H-K, Young, PM, Britton, WJ, Duke, CC & Traini, D 2014, 'A Rifapentine-Containing Inhaled Triple Antibiotic Formulation for Rapid Treatment of Tubercular Infection', Pharmaceutical Research, vol. 31, no. 5, pp. 1239-1253.
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Chan, KS, Ton-That, C, Vines, L, Choi, S, Phillips, MR, Svensson, BG, Jagadish, C & Wong-Leung, J 2014, 'Effects of high temperature annealing on defects and luminescence properties in H implanted ZnO', JOURNAL OF PHYSICS D-APPLIED PHYSICS, vol. 47, no. 34, pp. 1-6.
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The evolution of luminescence properties and voids formation with respect to annealing temperature in H implanted ZnO was investigated by depth-resolved cathodoluminescence spectroscopy (DRCLS), transmission electron microscopy and secondary ion mass spectrometry (SIMS). The annealing temperature is found to induce noticeable changes to the shape, size and empty volume density of the cavities. DRCLS results also reveal that the green emission is influenced by different annealing temperatures. In particular, the 600 °C anneal produces a strong quenching of the green emission in the implanted region, while after the 800 °C anneal a significant enhancement near the surface is observed. The annealing at 600 °C also results in an uncommon violet emission at ∼3.1 eV that is not observed after a higher annealing temperature. A clear correlation between the violet emission, vacancies and Li is revealed from comparison between the DRCLS intensities and SIMS data. © 2014 IOP Publishing Ltd.

Chaudhary, JP, Kondaveeti, S, Gupta, V, Prasad, K & Meena, R 2014, 'Preparation and functional evaluation of agarose derivatives', Journal of Applied Polymer Science, vol. 131, no. 16, pp. n/a-n/a.
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ABSTRACTA facile microwave‐assisted one‐pot synthesis of sodium carboxymethylagarose and calcium carboxymethylagarose from Gracilaria dura agarose (Ag) has been described. The process is user friendly, and the highest degree of substitution was obtained within 15 min compared with the conventional method, which requires more than 3 h. Solubility and gelling behavior of the modified Ag products were found to be dependent on degree of substitution of the products. The characterizations were done by using Fourier transform infrared spectroscopy, 1H‐ and 13C‐nuclear magnetic resonance spectroscopy, thermogravimetric analysis, scanning electron microscopy, Inductively coupled plasma spectrophotometry (ICP), rheology, conductometer analysis, and DNA gel electrophoresis. These agarose derivatives were easily soluble in water and exhibited low thermal hysteresis, improved conductivity, and improved the DNA resolution ability of the parent G. dura Ag hydrogels. These hydrogels may have potential applications in the areas including electrochemical devices, microbiology, biomedical, and pharmaceuticals fields. © 2014 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2014, 131, 40630.

Che, W, Parmentier, J, Seidel, P, Manetsch, M, Ramsay, EE, Alkhouri, H, Ge, Q, Armour, CL & Ammit, AJ 2014, 'Corticosteroids Inhibit Sphingosine 1-Phosphate–Induced Interleukin-6 Secretion from Human Airway Smooth Muscle via Mitogen-Activated Protein Kinase Phosphatase 1–Mediated Repression of Mitogen and Stress-Activated Protein Kinase 1', American Journal of Respiratory Cell and Molecular Biology, vol. 50, no. 2, pp. 358-368.
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Sphingosine 1-phosphate (S1P) is a bioactive sphingolipid that plays an important proinflammatory role in asthmatic airways. Corticosteroids are first-line antiinflammatories in asthma; however, their repressive effects on S1P-induced cytokine secretion have not been investigated. To address this, our in vitro study reveals the molecular mechanisms by which corticosteroids inhibit S1P-induced IL-6 expression in the pivotal immunomodulatory cell type, airway smooth muscle (ASM). We first uncover the cellular signaling pathways responsible: S1P activates a cyclic adenosine monophosphate/cAMP response-element-binding protein (CREB)/CRE-dependent pathway to induce IL-6 transcription, concomitant with stimulation of the mitogen-activated protein kinase (MAPK) superfamily and downstream mitogen and stress-activated protein kinase 1 (MSK1) and histone H3 phosphorylation. In this way, S1P stimulates parallel signaling pathways to induce IL-6 secretion via CRE-driven transcription of the IL-6 gene promoter in a relaxed chromatin environment achieved through histone H3 phosphorylation. Second, we investigated how corticosteroids mediate their repressive effects. The corticosteroid dexamethasone inhibits S1P-induced IL-6 protein secretion and mRNA expression, but CREB/CRE transrepression, inhibition of IL-6 mRNA stability, or subcellular relocation of MSK1 were not responsible for the repressive effects of dexamethasone. Rather, we show that dexamethasone rapidly induces up-regulation of the MAPK deactivator MAPK phosphatase 1 (MKP-1) and that MKP-1 blocks the MAPK-driven activation of MSK1 and phosphorylation of histone H3. This was confirmed by treatment with triptolide, an inhibitor of MKP-1 up-regulation, where repressive effects of corticosteroids were reversed. Our study reveals the molecular mechanism underlying the antiinflammatory capacity of corticosteroids to repress proinflammatory functions induced by the potent bioactive sphingolipid S1P in the lung.

Chejara, DR, Kondaveeti, S, Meena, R & Siddhanta, AK 2014, 'Antioxidant activity and phytochemical analysis of a few Indian seaweed species', Indian Journal of Geo-Marine Sciences, vol. 43, no. 4, pp. 507-518.
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Antioxidant activities of crude methanol extracts and fractions of the seaweed species viz. Bryopsis plumosa (BP), Dictyopteris australis (DA) and Gracilaria pudumadamensis (GP) of Indian waters were evaluated and correlated with their phytochemical contents. In DPPH assays the most promising antioxidant sample was the crude methanol extract (BPM), which was comparable with standard antioxidant BHT. In the superoxide radical activity assays no sample in the group was as active as BHT, however the promising ones were DAM, DAE and GPM, GPE, GPH (subscripts M, E and H stand for the respective methanol extracts and their ethyl acetate and hexane fractions). In the Fe2+ chelating activity assays EDTA showed far stronger activity than those of the promising samples. In reducing power assays BPM, BPE, and BPH showed comparable activity with BHT at a concentration 0.5 mg/mL. Thus these seaweed species would be of potential utility as a source of natural antioxidants.

Chen, C, Eamus, D, Cleverly, J, Boulain, N, Cook, P, Zhang, L, Cheng, L & Yu, Q 2014, 'Modelling vegetation water-use and groundwater recharge as affected by climate variability in an arid-zone Acacia savanna woodland', JOURNAL OF HYDROLOGY, vol. 519, pp. 1084-1096.
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Chen, H, Simar, D & Morris, MJ 2014, 'Maternal obesity impairs brain glucose metabolism and neural response to hyperglycemia in male rat offspring', Journal of Neurochemistry, vol. 129, no. 2, pp. 297-303.
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AbstractHypothalamic appetite regulators neuropeptide Y (NPY) and pro‐opiomelanocortin (POMC) are modulated by glucose. This study investigated how maternal obesity disturbs glucose regulation of NPY and POMC, and whether this deregulation is linked to abnormal hypothalamic glucose uptake‐lactate conversion. As post‐natal high‐fat diet (HFD) can exaggerate the effects of maternal obesity, its additional impact was also investigated. Female Sprague Dawley rats were fed a HFD (20 kJ/g) to model maternal obesity. At weaning, male pups were fed chow or HFD. At 9 weeks, in vivo hypothalamic NPY and POMC mRNA responses to acute hyperglycemia were measured; while hypothalami were glucose challenged in vitro to assess glucose uptake‐lactate release and related gene expression. Maternal obesity dampened in vivo hypothalamic NPY response to acute hyperglycemia, and lowered in vitro hypothalamic glucose uptake and lactate release. When challenged with 20 mM glucose, hypothalamic glucose transporter 1, monocarboxylate transporters, lactate dehydrogenase‐b, NPY and POMC mRNA expression were down‐regulated in offspring exposed to maternal obesity. Post‐natal HFD consumption reduced in vitro lactate release and monocarboxylate transporter 2 mRNA, but increased POMC mRNA levels when challenged with 20 mM glucose. Overall, maternal obesity produced stronger effects than post‐natal HFD consumption to impair hypothalamic glucose metabolism. However, they both disturbed NPY response to hyperglycemia, potentially leading to hyperphagia.

Chen, H, Simar, D, Pegg, K, Saad, S, Palmer, C & Morris, MJ 2014, 'Exendin-4 is effective against metabolic disorders induced by intrauterine and postnatal overnutrition in rodents', Diabetologia, vol. 57, no. 3, pp. 614-622.
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Aims/hypothesis: Maternal obesity leads to increased adiposity, hyperlipidaemia and glucose intolerance in offspring. The analogue of glucagon-like peptide-1, exendin-4 (Ex-4), has been shown to induce weight loss in both adolescence and adulthood. We hypothesised that, in rats, daily injection of Ex-4 would reduce body fat and improve metabolic disorders in offspring from obese dams, especially those consuming a high-fat diet (HFD). Methods: Female Sprague Dawley rats were fed chow or an HFD for 5 weeks before mating, and throughout gestation and lactation. At postnatal day 20, male pups from HFD-fed mothers were weaned onto chow or HFD and those from chow-fed mothers were fed chow. Within each dietary group, half of the pups were injected with Ex-4 (15 μg/kg/day i.p.) for 6 weeks, while the other half received saline. Results: Maternal obesity alone or combined with postweaning HFD consumption led to increased adiposity, hyperinsulinaemia, hyperlipidaemia, inflammation and impaired regulation of hypothalamic appetite regulators by glucose in offspring, while glucose intolerance was only observed in HFD-fed rats from obese dams. Ex-4 injection significantly reduced adiposity, hyperlipidaemia and insulin resistance in HFD-fed rats from obese dams. It also restored glucose tolerance and the lipid-lowering effect of blood glucose. However, Ex-4 did not change hypothalamic appetite regulation or the response of appetite regulators to hyperglycaemia. Liver and adipose inflammatory cytokine expression was significantly reduced by Ex-4. Conclusions/interpretation: Ex-4 reversed the detrimental impact of maternal obesity on lipid and glucose metabolism in offspring regardless of diet, supporting its potential application in reducing metabolic disorders in high-risk populations. © 2013 Springer-Verlag Berlin Heidelberg.

Chen, L, Ge, Q, Tjin, G, Alkhouri, H, Deng, L, Brandsma, C-A, Adcock, I, Timens, W, Postma, D, Burgess, JK, Black, JL & Oliver, BGG 2014, 'Effects of cigarette smoke extract on human airway smooth muscle cells in COPD', European Respiratory Journal, vol. 44, no. 3, pp. 634-646.
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We hypothesised that the response to cigarette smoke in airway smooth muscle (ASM) cells from smokers with chronic obstructive pulmonary disease (COPD) would be intrinsically different from smokers without COPD, producing greater pro-inflammatory mediators and factors relating to airway remodelling.ASM cells were obtained from smokers with or without COPD, and then stimulated with cigarette smoke extract (CSE) or transforming growth factor-β1. The production of chemokines and matrix metalloproteinases (MMPs) were measured by ELISA, and the deposition of collagens by extracellular matrix ELISA. The effects of CSE on cell attachment and wound healing were measured by toluidine blue attachment and cell tracker green wound healing assays.CSE increased the release of CXCL8 and CXCL1 from human ASM cells, and cells from smokers with COPD produced more CSE-induced CXCL1. The production of MMP-1, -3 and -10, and the deposition of collagen VIII alpha 1 (COL8A1) were increased by CSE, especially in the COPD group which had higher production of MMP-1 and deposition of COL8A1. CSE decreased ASM cell attachment and wound healing in the COPD group only.ASM cells from smokers with COPD were more sensitive to CSE stimulation, which may explain, in part, why some smokers develop COPD.

Chen, P, Zhou, J, Fang, Z, Wang, J, Xu, B, Tan, D, Khisro, SN & Qiu, J 2014, 'Near-mid infrared emission in Ce3+ and Tm3+ co-doped oxyfluoride glasses by excited at different wavelengths light', Journal of Non-Crystalline Solids, vol. 391, pp. 49-53.
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A novel approach has been proposed to realize enhanced near-mid infrared emission in Ce3 + and Tm3 + co-doped oxyfluoride glasses excited at different wavelengths, whereby Ce3 + absorbs the photons in ultraviolet region and transfers the energy to Tm3 +, while Tm3 + converts the energy in visible and near infrared region into near-mid infrared region. For the purpose to achieve efficient near-mid infrared emission, ligand field theory has been adopted to optimize the glass host composition. The excitation, emission, time-resolved emission spectra and fluorescence decay curves have been measured to investigate the energy transfer (ET) from Ce3 + to Tm3 + and the generation mechanism of near-mid infrared emission. This approach will be of reference value for designing the gain medium of the near-mid infrared laser excited directly by the sunlight.

Chen, S, Bao, P, Huang, X, Sun, B & Wang, G 2014, 'Hierarchical 3D mesoporous silicon@graphene nanoarchitectures for lithium ion batteries with superior performance', NANO RESEARCH, vol. 7, no. 1, pp. 85-94.
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Silicon has been recognized as the most promising anode material for high capacity lithium ion batteries. However, large volume variations during charge and discharge result in pulverization of Si electrodes and fast capacity loss on cycling. This drawback of Si electrodes can be overcome by combination with well-organized graphene foam. In this work, hierarchical three-dimensional carbon-coated mesoporous Si nanospheres@graphene foam (C@Si@GF) nanoarchitectures were successfully synthesized by a thermal bubble ejection assisted chemical-vapor-deposition and magnesiothermic reduction method. The morphology and structure of the as-prepared nanocomposites were characterized by field emission scanning electron microscopy, transmission electron microscopy and Raman spectroscopy. When employed as anode materials in lithium ion batteries, C@Si@GF nanocomposites exhibited superior electrochemical performance including a high specific capacity of 1,200 mAh/g at the current density of 1 A/g, excellent high rate capabilities and an outstanding cyclability. Post-mortem analyses identified that the morphology of 3D C@Si@GF electrodes after 200 cycles was well maintained. The synergistic effects arising from the combination of mesoporous Si nanospheres and graphene foam nanoarchitectures may address the intractable pulverization problem of Si electrode. [Figure not available: see fulltext.] © 2014 Tsinghua University Press and Springer-Verlag Berlin Heidelberg.

Chen, S, Huang, X, Liu, H, Sun, B, Yeoh, W, Li, K, Zhang, J & Wang, G 2014, '3D Hyperbranched Hollow Carbon Nanorod Architectures for High-Performance Lithium-Sulfur Batteries', ADVANCED ENERGY MATERIALS, vol. 4, no. 8, p. 1301761.
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Lithium-sulfur batteries have been plagued for a long time by low Coulombic efficiency, fast capacity loss, and poor high rate performance. Here, the synthesis of 3D hyperbranched hollow carbon nanorod encapsulated sulfur nanocomposites as cathode materials for lithium-sulfur batteries is reported. The sulfur nanocomposite cathodes deliver a high specific capacity of 1378 mAh g-1 at a 0.1C current rate and exhibit stable cycling performance. The as-prepared sulfur nanocomposites also achieve excellent high rate capacities and cyclability, such as 990 mAh g-1 at 1C, 861 mAh g -1 at 5C, and 663 mAh g-1 at 10C, extending to more than 500 cycles. The superior electrochemical performance are ascribed to the unique 3D hyperbranched hollow carbon nanorod architectures and high length/radius aspect ratio of the carbon nanorods, which can effectively prevent the dissolution of polysulfides, decrease self-discharge, and confine the volume expansion on cycling. High capacity, excellent high-rate performance, and long cycle life render the as-developed sulfur/carbon nanorod nanocomposites a promising cathode material for lithium-sulfur batteries. 3D hyperbranched carbon nanorod-sulfur nanocomposites are synthesized and applied as cathode materials for lithium-sulfur batteries. The composite materials deliver high specific capacity, excellent high rate capability, and extended cycle life. The superior performance is attributed to the nanomaze architecture and high aspect ratio of carbon nanorods, which suppress the dissolution of polysulfides and confine volume expansion. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Chen, S, Huang, X, Liu, H, Sun, B, Yeoh, W, Li, K, Zhang, J & Wang, G 2014, '3D Hyperbranched Hollow Carbon Nanorod Encapsulated Sulfur Composites for Lithium-Sulfur Batteries with Superior Electrochemical Performance', ECS Meeting Abstracts, vol. MA2014-04, no. 3, pp. 511-511.
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Lithium-sulfur batteries have been plagued for a long time by the low Coulombic efficiency, fast capacity loss and poor high rate performance. Herein, we report the synthesis of graphitic hyperbranched hollow carbon nanorods encapsulated sulfur composites as cathode materials for lithium-sulfur batteries. The sulfur composite cathodes, approximate 1 mg for each electrode, deliver a high specific capacity of 1378 mAh/g at 0.1C current rate and exhibit stable cycling performance. The as-prepared cathode materials also achieve excellent high rate capacities and cyclability, such as 990 mAh/g at 1C, 861 mAh/g at 5C and 663 mAh/g at 10C, extending to more than 500 cycles. The superior electrochemical performances could be ascribed to the unique graphitic hyperbranched hollow carbon nanorods architecture and high length/radius aspect ratio of carbon nanorods, which can effectively prevent the dissolution of polysulfides, decrease self-discharge and confine the volume expansion on cycling. High capacity, excellent high-rate performance and long cycle life render the as-developed sulfur/carbon nanorod composites as a promising cathode material for lithium-sulfur batteries.

Chen, S, Huang, X, Liu, H, Sun, B, Yeoh, W, Li, K, Zhang, J & Wang, G 2014, 'Batteries: 3D Hyperbranched Hollow Carbon Nanorod Architectures for High‐Performance Lithium‐Sulfur Batteries (Adv. Energy Mater. 8/2014)', Advanced Energy Materials, vol. 4, no. 8, pp. n/a-n/a.
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Chen, S, Huang, X, Sun, B, Zhang, J, Liu, H & Wang, G 2014, 'Multi-shelled hollow carbon nanospheres for lithium-sulfur batteries with superior performances', JOURNAL OF MATERIALS CHEMISTRY A, vol. 2, no. 38, pp. 16199-16207.
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© the Partner Organisations 2014. Lithium-sulfur batteries are regarded as a promising energy storage system. However, they are plagued by rapid capacity decay, low coulombic efficiency, a severe shuttle effect and low sulfur loading in cathodes. To address these problems, effective carriers are highly demanded to encapsulate sulfur and extend the cycle life. Here, we report an aqueous emulsion approach and in situ sulfur impregnation to synthesize multi-shelled hollow carbon nanosphere-encapsulated sulfur composites with a high percentage of sulfur loading (86 wt%). When applied as cathodes in lithium-sulfur batteries, the composite materials delivered a high specific capacity of 1350 mA h g-1and excellent capacity retention (92% for 200 cycles). Further measurements at high current densities also demonstrate significantly enhanced cyclability and high rate capability. This journal is

Chen, Y, Bogema, DR, Barchia, IM & Herron, GA 2014, 'Quantification of the Pirimicarb Resistance Allele Frequency in Pooled Cotton Aphid (Aphis gossypii Glover) Samples by TaqMan SNP Genotyping Assay', PLOS ONE, vol. 9, no. 3, pp. 1-12.
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Pesticide resistance monitoring is a crucial part to achieving sustainable integrated pest management (IPM) in agricultural production systems. Monitoring of resistance in arthropod populations is initially performed by bioassay, a method that detects a phenotypic response to pesticides. Molecular diagnostic assays, offering speed and cost improvements, can be developed when the causative mutation for resistance has been identified. However, improvements to throughput are limited as genotyping methods cannot be accurately applied to pooled DNA. Quantifying an allele frequency from pooled DNA would allow faster and cheaper monitoring of pesticide resistance.We demonstrate a new method to quantify a resistance allele frequency (RAF) from pooled insects via TaqMan assay by using raw fluorescence data to calculate the transformed fluorescence ratio k' at the inflexion point based on a four parameter sigmoid curve. Our results show that k' is reproducible and highly correlated with RAF (r >0.99). We also demonstrate that k' has a non-linear relationship with RAF and that five standard points are sufficient to build a prediction model. Additionally, we identified a non-linear relationship between runs for k', allowing the combination of samples across multiple runs in a single analysis.The transformed fluorescence ratio (k') method can be used to monitor pesticide resistance in IPM and to accurately quantify allele frequency from pooled samples. We have determined that five standards (0.0, 0.2, 0.5, 0.8, and 1.0) are sufficient for accurate prediction and are statistically-equivalent to the 13 standard points used experimentally.

Chen, Y, Zhang, H, Xue, H, Hu, X, Wang, G & Wang, C 2014, 'Construction of a non-enzymatic glucose sensor based on copolymer P4VP-co-PAN and Fe2O3 nanoparticles', Materials Science and Engineering: C, vol. 35, pp. 420-425.
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An electrochemical sensor based on a copolymer poly(4-vinylpyridine)-co-poly(acrylonitrile), P4VP-co-PAN, and Fe2O3 nanoparticle film modified glassy carbon electrode was developed for the determination of glucose. We studied the response of glucosewith the proposed electrode, and determined the optimumconditions by changing the potential, pH and P4VP-co-PAN. The current responsemeasurementswere performed in PBS (c = 0.1 M) with a potential of 0.7 V. The current response of this glucose sensor showed a linear relationship with the concentration in the range of 2.5 µM0.58 mM (r = 0.997). The experimental results demonstrate that this method has suchmerits as simple operation, lowcost, high sensitivity, long termstability and good reproducibility, with satisfactory results.

Chen, Z, Ngo, HH, Guo, W, Lim, R, Wang, XC, O'Halloran, K, Listowski, A, Corby, N & Miechel, C 2014, 'A comprehensive framework for the assessment of new end uses in recycled water schemes', SCIENCE OF THE TOTAL ENVIRONMENT, vol. 470, pp. 44-52.
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Nowadays, recycled water has provided sufficient flexibility to satisfy short-term freshwater needs and increase the reliability of long-term water supplies in many water scarce areas, which becomes an essential component of integrated water resources management. However, the current applications of recycled water are still quite limited that are mainly associated with non-potable purposes such as irrigation, industrial uses, toilet flushing and car washing. There is a large potential to exploit and develop new end uses of recycled water in both urban and rural areas. This can greatly contribute to freshwater savings, wastewater reduction and water sustainability. Consequently, the paper identified the potentials for the development of three recycled water new end uses, household laundry, livestock feeding and servicing, and swimming pool, in future water use market. To validate the strengths of these new applications, a conceptual decision analytic framework was proposed. This can be able to facilitate the optional management strategy selection process and thereafter provide guidance on the future end use studies within a larger context of the community, processes, and models in decision-making. Moreover, as complex evaluation criteria were selected and taken into account to narrow down the multiple management alternatives, the methodology can successfully add transparency, objectivity and comprehensiveness to the assessment. Meanwhile, the proposed approach could also allow flexibility to adapt to particular circumstances of each case under study. © 2013 Elsevier B.V.

Chen, Z, Ngo, HH, Guo, W, Pham, TTN, Lim, R, Wang, XC, Miechel, C, O' Halloran, K, Listowski, A & Corby, N 2014, 'A new optional recycled water pre-treatment system prior to use in the household laundry', SCIENCE OF THE TOTAL ENVIRONMENT, vol. 476, pp. 513-521.
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With a constantly growing population, water scarcity becomes the limiting factor for further social and economic growth. To achieve a partial reduction in current freshwater demands and lessen the environmental loadings, an increasing trend in the water market tends to adopt recycled water for household laundries as a new recycled water application. The installation of a small pre-treatment unit for water purification can not only further improve the recycled water quality, but also be viable to enhance the public confidence and acceptance level on recycled water consumption. Specifically, this paper describes column experiments conducted using a 550. mm length bed of zeolite media as a one-dimensional flow reactor. The results show that the zeolite filter system could be a simple low-cost pre-treatment option which is able to significantly reduce the total hardness level of recycled water via effective ion exchange. Additionally, depending on the quality of recycled water required by end users, a new by-pass controller using a three-level operation switching mechanism is introduced. This approach provides householders sufficient flexibility to respond to different levels of desired recycled water quality and increase the reliability of long-term system operation. These findings could be beneficial to the smooth implementation of new end uses and expansion of the potential recycled water market. The information could also offer sound suggestions for future research on sustainable water management and governance. © 2014 Elsevier B.V.

Cheng, G, Wu, H, Yang, Z, Liao, J, Lai, S, Qiu, J & Song, Z 2014, 'Upconversion emission properties of CeO₂: Tm³⁺, Yb³⁺ inverse opal photonic crystals', Modern Physics Letters B, vol. 28, no. 27, pp. 1450218-1450218.
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The ordered and disordered templates were assembled by vertical deposition of polystyrene microspheres. The CeO 2: Tm 3+, Yb 3+ precursor solution was used to infiltrate into the voids of the ordered and disordered templates, respectively. Then the ordered and disordered templates were calcined at 950°C in an air furnace, and the CeO 2: Tm 3+, Yb 3+ inverse opals were obtained. The upconversion emissions from CeO 2: Tm 3+, Yb 3+ inverse opals were suppressed due to the photon trapping caused by Bragg reflection of lattice planes when the upconversion emission band was in the range of the photonic band gaps in the inverse opals.

Cheng, L, Zhang, L, Wang, Y-P, Yu, Q & Eamus, D 2014, 'Quantifying the effects of elevated CO2 on water budgets by combining FACE data with an ecohydrological model', ECOHYDROLOGY, vol. 7, no. 6, pp. 1574-1588.
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© 2014 John Wiley & Sons, Ltd. Response of leaf area index (LAI) is the key determinant for predicting impacts of the elevated CO2 (eCO2) on water budgets. Importance of the changes in functional attributes of vegetation associated with eCO2 for predicting responses of LAI has rarely been addressed. In this study, the WAter Vegetation Energy and Solute (WAVES) model was applied to simulate ecohydrological effects of the eCO2 at two free-air CO2 enrichment (FACE) experimental sites with contrasting vegetation. One was carried out by the Oak Ridge National Laboratory on the forest (ORNL FACE). The other one was conducted by the University of Minnesota on the grass (BioCON FACE). Results demonstrated that changes in functional attributes of vegetation (including reduction in specific leaf area, changes in carbon assimilation and allocation characteristics) and availability of nutrients are important for reproducing the responses of LAI, transpiration and soil moisture at both sites. Predicted LAI increased slightly at both sites because of fertilization effects of the eCO2. Simulated transpiration decreased 10·5% at ORNL site and 13·8% at BioCON site because of reduction in the stomatal conductance. Predicted evaporation from interception and soil surface increased slightly (<1·0mmyear-1) at both sites because of increased LAI and litter production, and increased soil moisture resulted from reduced transpiration. All components of run-off were predicted to increase because of significant decrease in transpiration. Simulated mean annual evapotranspiration decreased about 8·7% and 10·8%, and mean annual run-off increased about 11·1% (59·3mmyear-1) and 9·5% (37·6mmyear-1) at the ORNL and BioCON FACE sites, respectively.

Cheng, L, Zhang, L, Wang, Y-P, Yu, Q, Eamus, D & O'Grady, A 2014, 'Impacts of elevated CO2, climate change and their interactions on water budgets in four different catchments in Australia', JOURNAL OF HYDROLOGY, vol. 519, pp. 1350-1361.
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Chevalier, N, Thorburn, AN, Macia, L, Tan, J, Juglair, L, Yagita, H, Yu, D, Hansbro, PM & Mackay, CR 2014, 'Inflammation and Lymphopenia Trigger Autoimmunity by Suppression of IL-2–Controlled Regulatory T Cell and Increase of IL-21–Mediated Effector T Cell Expansion', The Journal of Immunology, vol. 193, no. 10, pp. 4845-4858.
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AbstractThe dynamic interplay between regulatory T cells (Tregs) and effector T cells (Teffs) governs the balance between tolerance and effector immune responses. Perturbations of Treg frequency and function or imbalances in Treg/Teff levels are associated with the development of autoimmunity. The factors that mediate these changes remain poorly understood and were investigated in this study in murine autoimmune arthritis. Tregs displayed a stable phenotype in arthritic mice and were fully functional in in vitro suppression assays. However, their expansion was delayed relative to Teffs (T follicular helper cells and Th17 cells) during the early stages of autoimmune reactivity. This imbalance is likely to have led to insufficient Treg control of Teffs and induced autoimmunity. Moreover, a counterregulatory and probably IL-7–driven increase in thymic Treg production and recruitment to inflamed tissues was too slow for disease prevention. Increased Teff over Treg expansion was further aggravated by inflammation and lymphopenia. Both these conditions contribute to autoimmune pathogenesis and were accompanied by decreases in the availability of IL-2 and increases in levels of IL-21. IL-2 neutralization or supplementation was used to show that Treg expansion mainly depended on this cytokine. IL-21R−/− cells were used to demonstrate that IL-21 promoted the maintenance of Teffs. Thus, at inflammatory sites in experimental arthritis, a deficit in IL-2 hampers Treg proliferation, whereas exaggerated IL-21 levels overwhelm Treg control by supporting Teff expansion. This identifies IL-2 and IL-21 as targets for manipulation in therapies for autoimmunity.

Chew, SC, Kundukad, B, Seviour, T, van der Maarel, JRC, Yang, L, Rice, SA, Doyle, P & Kjelleberg, S 2014, 'Dynamic Remodeling of Microbial Biofilms by Functionally Distinct Exopolysaccharides', mBio, vol. 5, no. 4.
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ABSTRACT Biofilms are densely populated communities of microbial cells protected and held together by a matrix of extracellular polymeric substances. The structure and rheological properties of the matrix at the microscale influence the retention and transport of molecules and cells in the biofilm, thereby dictating population and community behavior. Despite its importance, quantitative descriptions of the matrix microstructure and microrheology are limited. Here, particle-tracking microrheology in combination with genetic approaches was used to spatially and temporally study the rheological contributions of the major exopolysaccharides Pel and Psl in Pseudomonas aeruginosa biofilms. Psl increased the elasticity and effective cross-linking within the matrix, which strengthened its scaffold and appeared to facilitate the formation of microcolonies. Conversely, Pel reduced effective cross-linking within the matrix. Without Psl, the matrix becomes more viscous, which facilitates biofilm spreading. The wild-type biofilm decreased in effective cross-linking over time, which would be advantageous for the spreading and colonization of new surfaces. This suggests that there are regulatory mechanisms to control production of the exopolysaccharides that serve to remodel the matrix of developing biofilms. The exopolysaccharides were also found to have profound effects on the spatial organization and integration of P. aeruginosa in a mixed-species biofilm model of P. aeruginosa - Staphylococcus aureus . Pel was required for close association of the two species in mixed-species microc...

Chivers, WJ, Gladstone, W, Herbert, RD & Fuller, MM 2014, 'Predator-prey systems depend on a prey refuge', JOURNAL OF THEORETICAL BIOLOGY, vol. 360, pp. 271-278.
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Models of near-exclusive predatorprey systems such as that of the Canadian lynx and snowshoe hare have included factors such as a second prey species, a Holling Type II predator response and climatic or seasonal effects to reproduce sub-sets of six signature patterns in the empirical data. We present an agent-based model which does not require the factors or constraints of previous models to reproduce all six patterns in persistent populations. Our parsimonious model represents a generalised predator and prey species with a small prey refuge. The lack of the constraints of previous models, considered to be important for those models, casts doubt on the current hypothesised mechanisms of exclusive predatorprey systems. The implication for management of the lynx, a protected species, is that maintenance of an heterogeneous environment offering natural refuge areas for the hare is the most important factor for the conservation of this species.

Cho, HR, Kim, DH, Kim, D, Doble, P, Bishop, D, Hare, D, Park, C-K, Moon, WK, Han, MH & Choi, SH 2014, 'Malignant Glioma: MR Imaging by Using 5-Aminolevulinic Acid in an Animal Model', RADIOLOGY, vol. 272, no. 3, pp. 720-730.
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Cho, KT, Richardson, MM, Kirkbride, KP, McNevin, D, Nelson, M, Pianca, D, Roffey, P & Gahan, ME 2014, 'Recovery and identification of bacterial DNA from illicit drugs', Forensic Science International, vol. 235, pp. 78-85.
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Cho, Y, Turner, ND, Davidson, LA, Chapkin, RS, Carroll, RJ & Lupton, JR 2014, 'Colon cancer cell apoptosis is induced by combined exposure to the n-3 fatty acid docosahexaenoic acid and butyrate through promoter methylation', Experimental Biology and Medicine, vol. 239, no. 3, pp. 302-310.
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DNA methylation and histone acetylation contribute to the transcriptional regulation of genes involved in apoptosis. We have demonstrated that docosahexaenoic acid (DHA, 22:6 n-3) and butyrate enhance colonocyte apoptosis. To determine if DHA and/or butyrate elevate apoptosis through epigenetic mechanisms thereby restoring the transcription of apoptosis-related genes, we examined global methylation; gene-specific promoter methylation of 24 apoptosis-related genes; transcription levels of Cideb, Dapk1, and Tnfrsf25; and global histone acetylation in the HCT-116 colon cancer cell line. Cells were treated with combinations of (50 µM) DHA or linoleic acid (18:2 n-6), (5 mM) butyrate or an inhibitor of DNA methyltransferases, and 5-aza-2′-deoxycytidine (5-Aza-dC, 2 µM). Among highly methylated genes, the combination of DHA and butyrate significantly reduced methylation of the proapoptotic Bcl2l11, Cideb, Dapk1, Ltbr, and Tnfrsf25 genes compared to untreated control cells. DHA treatment reduced the methylation of Cideb, Dapk1, and Tnfrsf25. These data suggest that the induction of apoptosis by DHA and butyrate is mediated, in part, through changes in the methylation state of apoptosis-related genes.

Choi, AH, Conway, RC & Ben-Nissan, B 2014, 'Finite-Element Modeling and Analysis in Nanomedicine and Dentistry', Nanomedicine, vol. 9, no. 11, pp. 1681-1695.
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This article aims to provide a brief background to the current applications of finite-element analysis (FEA) in nanomedicine and dentistry. FEA was introduced in orthopedic biomechanics in the 1970s in order to assess the stresses and deformation in human bones during functional loadings and in the design and analysis of implants. Since then, it has been applied with great frequency in orthopedics and dentistry in order to analyze issues such as implant design, bone remodeling and fracture healing, the mechanical properties of biomedical coatings on implants and the interactions at the bone–implant interface. More recently, FEA has been used in nanomedicine to study the mechanics of a single cell and to gain fundamental insights into how the particulate nature of blood influences nanoparticle delivery.

Choi, M, Ham, G, Jin, B-S, Lee, S-M, Lee, YM, Wang, G & Kim, H-S 2014, 'Ultra-thin Al2O3 coating on the acid-treated 0.3Li2MnO3⋅0.7LiMn0.60Ni0.25Co0.15O2 electrode for Li-ion batteries', Journal of Alloys and Compounds, vol. 608, pp. 110-117.
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The Li and Mn-rich layered composites represented by Li2MnO3LiMO2 has been attracting great interests owing to its exceptional high capacity (P250 mA h g1) and enhanced structural stability. In order to improve the initial coulombic efficiency and cyclability of the composites, the material has been activated by an acid-treatment and coated with an Al2O3 using an atomic layer deposition (ALD). The acid-treated electrode showed a higher discharge capacity than the as-prepared electrode. The alumina-coated electrode provided an improved specific capacity of the electrode but also cycling stability, when compared with the bare electrode. The electrode coated with the alumina could lead to a decrease in undesirable reactions, thereby acting as a stable protecting layer that could quickly transport Li+ ions during charge and discharge process.

Choi, S, Johnson, BC, Castelletto, S, Ton-That, C, Phillips, MR & Aharonovich, I 2014, 'Single photon emission from ZnO nanoparticles', APPLIED PHYSICS LETTERS, vol. 104, no. 26.
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Room temperature single photon emitters are very important resources for photonics and emerging quantum technologies. In this work, we study single photon emission from defect centers in 20 nm zinc oxide (ZnO) nanoparticles. The emitters exhibit bright broadband fluorescence in the red spectral range centered at 640 nm with polarized excitation and emission. The studied emitters showed continuous blinking; however, bleaching can be suppressed using a polymethyl methacrylate coating. Furthermore, hydrogen termination increased the density of single photon emitters. Our results will contribute to the identification of quantum systems in ZnO. © 2014 AIP Publishing LLC.

Chou, J, Hao, J, Kuroda, S, Ben-Nissan, B, Milthopre, B & Otsuka, M 2014, 'Bone regeneration of calvarial defect using marine calcareous-derived beta-tricalcium phosphate macrospheres', Journal of Tissue Engineering, vol. 5, pp. 204173141452344-204173141452344.
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The aim of this study was to examine the bone regeneration properties of beta-tricalcium phosphate hydrothermally converted from foraminifera carbonate exoskeleton in the repair of rat calvarial defect. These natural materials possess unique interconnected porous network with uniform pore size distribution, which can be potentially advantageous. In total, 20 adult male Wistar rats received full-thickness calvarial defect with a diameter of 5 mm. The rate of newly formed bone was measured radiologically by X-ray and micro-computed tomography and by histologic examination. After 2 weeks, the beta-tricalcium phosphate group exhibited full closure of the defect site, while control group remained unrestored at the end of the 6-week experimentation. It was observed that the newly regenerated bone thickened over the course of the experiment in the beta-tricalcium phosphate group. No soft tissue reaction was observed around the beta-tricalcium phosphate implant and the rats remained healthy. These results showed that repair of the calvarial defect can be achieved by biomimetic beta-tricalcium phosphate macrospheres, which hold potential for application as bone grafts for bone augmentation surgeries.

Chou, J, Valenzuela, S, Green, DW, Kohan, L, Milthorpe, B, Otsuka, M & Ben-Nissan, B 2014, 'Antibiotic Delivery Potential of Nano- and Micro-Porous Marine Structure-Derived β-Tricalcium Phosphate Spheres for Medical Applications', Nanomedicine, vol. 9, no. 8, pp. 1131-1139.
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Aims: This study gives a detailed evaluation of the antibiotic potential of a marine structure-based new drug delivery system produced by hydrothermally converting foraminifera exoskeletons to β-tricalcium phosphate (β-TCP) to treat clinical strain Staphylococcus aureus (MW2). Materials & methods: Foraminifera precursor materials were hydrothermally converted at 250°C for 48 h to produce β-TCP and loaded with gentamicin sulfate by adsorption for 24 h. The physicochemical properties of the material were characterized by scanning electron microscopy, powder x-ray diffraction and for pore size distribution profiles. The antibacterial efficacy of the system was tested for inhibition of S. aureus growth and in vitro cellular behavior were tested with human osteoblast cells (MG63) for cell viability. Discussion: Pore size distribution profiles showed that the structure allows the uniform distribution of nanopores of 1.5 nm and micropores of approximately 5 µm. The in vitro release profile indicates an initial burst release of 5% of total incorporated gentamicin. A time-delayed antibacterial efficacy test was designed to introduce the bacteria at predetermined time intervals from 0 to 60 min and showed that gentamicin prevents S. aureus grown in the same culture within 30 min, with no evidence of bacterial regrowth within 24 h. Human osteoblast cell (MG63) studies showed no detrimental effect on cell viability. Conclusion: In the light of these results nano- and micro-pores containing β-TCP spheres show promise as potential bone void filler particles with antibacterial effects.Original submitted 7 February 2013; Revised submitted 9 May 2013

Chou, J, Valenzuela, SM, Santos, J, Bishop, D, Milthorpe, B, Green, DW, Otsuka, M & Ben-Nissan, B 2014, 'Strontium- and magnesium-enriched biomimeticβ-TCP macrospheres with potential for bone tissue morphogenesis', Journal of Tissue Engineering and Regenerative Medicine, vol. 8, no. 10, pp. 771-778.
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Chowdhury, PR, McKinnon, J, Wyrsch, E, Hammond, JM, Charles, IG & Djordjevic, SP 2014, 'Genomic interplay in bacterial communities: implications for growth promoting practices in animal husbandry', FRONTIERS IN MICROBIOLOGY, vol. 5, no. 5, pp. 394-394.
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Thediscoveryofantibioticsheraldedthestartofa“GoldenAge”inthehistoryofmedicine.Overtheyears,theuseofantibioticsextendedbeyondmedicalpracticeintoanimalhusbandry,aquacultureandagriculture.Now,however,wefacetheworldwidethreatofdiseasescausedbypathogenicbacteriathatareresistanttoallexistingmajorclassesofantibiotic,reflectingthepossibilityofanendtotheantibioticera.Theseriousnessofthethreatisunderscoredbytheseverelylimitedproductionofnewclassesofantibiotics.Evolutionofbacteriaresistanttomultipleantibioticsresultsfromtheinherentgeneticcapabilitythatbacteriahavetoadaptrapidlytochangingenvironmentalconditions.Consequently,underantibioticselectionpressures,bacteriahaveacquiredresistancetoallclassesofantibiotics,sometimesveryshortlyaftertheirintroduction.Arguably,theevolutionandrapiddisseminationofmultipledrugresistantgenesen-masseacrossmicrobialpathogensisoneofthemostseriousthreatstohumanhealth.Inthiscontext,effectivesurveillancestrategiestotrackthedevelopmentofresistancetomultipleantibioticsarevitaltomanagingglobalinfectioncontrol.Thesesurveillancestrategiesarenecessaryfornotonlyhumanhealthbutalsoforanimalhealth,aquacultureandplantproduction.Shortfallsinthepresentsurveillancestrategiesneedtobeidentified.Raisingawarenessofthegeneticeventsthatpromoteco-selectionofresistancetomultipleantimicrobialsisanimportantprerequisitetothedesignandimplementationofmolecularsurveillancestrategies.Inthisreviewwewilldiscusshowlateralgenetransfer(LGT),drivenbytheuseoflow-doseantibioticsinanimalhusbandry,haslikelyplayedasignificantroleintheevolutionofmultipledrugresistance(MDR)inGram-negativebacteriaandhascomplicatedmolecularsurveillancestrategiesadoptedforpredictingimminentresistancethreats.

Chung, L, Moore, K, Phillips, L, Boyle, FM, Marsh, DJ & Baxter, RC 2014, 'Novel serum protein biomarker panel revealed by mass spectrometry and its prognostic value in breast cancer', Breast Cancer Research, vol. 16, no. 3.
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Abstract Introduction Serum profiling using proteomic techniques has great potential to detect biomarkers that might improve diagnosis and predict outcome for breast cancer patients (BC). This study used surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF) mass spectrometry (MS) to identify differentially expressed proteins in sera from BC and healthy volunteers (HV), with the goal of developing a new prognostic biomarker panel. Methods Training set serum samples from 99 BC and 51 HV subjects were applied to four adsorptive chip surfaces (anion-exchange, cation-exchange, hydrophobic, and metal affinity) and analyzed by time-of-flight MS. For validation, 100 independent BC serum samples and 70 HV samples were analyzed similarly. Cluster analysis of protein spectra was performed to identify protein patterns related to BC and HV groups. Univariate and multivariate statistical analyses were used to develop a protein panel to distinguish breast cancer sera from healthy sera, and its prognostic potential was evaluated. Results From 51 protein peaks that were significantly up- or downregulated in BC patients by univariate analysis, binary logistic regression yielded five protein peaks that together classified BC and HV with a receiver operating characteristic (ROC) area-under-the-curve value of 0.961. Validation on an independent patient cohort confirmed the five-protein parameter (ROC value 0.939). The five-protein parameter showed positive association with large tumor size (P = 0.018) and lymph node involvement (P

Cleverley, RM, Barrett, JR, Baslé, A, Bui, NK, Hewitt, L, Solovyova, A, Xu, Z-Q, Daniel, RA, Dixon, NE, Harry, EJ, Oakley, AJ, Vollmer, W & Lewis, RJ 2014, 'Structure and function of a spectrin-like regulator of bacterial cytokinesis', Nature Communications, vol. 5, no. 1, pp. 1-10.
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AbstractBacterial cell division is facilitated by a molecular machine—the divisome—that assembles at mid-cell in dividing cells. The formation of the cytokinetic Z-ring by the tubulin homologue FtsZ is regulated by several factors, including the divisome component EzrA. Here we describe the structure of the 60-kDa cytoplasmic domain of EzrA, which comprises five linear repeats of an unusual triple helical bundle. The EzrA structure is bent into a semicircle, providing the protein with the potential to interact at both N- and C-termini with adjacent membrane-bound divisome components. We also identify at least two binding sites for FtsZ on EzrA and map regions of EzrA that are responsible for regulating FtsZ assembly. The individual repeats, and their linear organization, are homologous to the spectrin proteins that connect actin filaments to the membrane in eukaryotes, and we thus propose that EzrA is the founding member of the bacterial spectrin family.

Coil, D, Jospin, G & Darling, AE 2014, 'A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data', Bioinformatics, vol. 31, no. 4, pp. 587-589.
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Motivation: Open-source bacterial genome assembly remains inaccessible tomany biologists due to its complexity. Few software solutions exist that arecapable of automating all steps in the process of de novo genome assembly fromIllumina data. Results: A5-miseq can produce high quality microbial genome assemblies fromas little as 20-fold sequence data coverage on a laptop computer without anyparameter tuning. A5-miseq does this by automating the process of adaptertrimming, quality filtering, error correction, contig and scaffold generation,and detection of misassemblies. Unlike the original A5 pipeline, A5-miseq canuse long reads from the Illumina MiSeq, use read pairing information duringcontig generation, and includes several improvements to read trimming. Togetherthese changes result in substantially improved assemblies that recover a morecomplete set of reference genes than previous methods. Availability: A5-miseq is licensed under the GPL open source license. Sourcecode and precompiled binaries for Mac OS X 10.6+ and Linux 2.6.15+ areavailable from http://sourceforge.net/projects/ngopt

Corporal-Lodangco, IL, Richman, MB, Leslie, LM & Lamb, PJ 2014, 'Cluster Analysis of North Atlantic Tropical Cyclones', Procedia Computer Science, vol. 36, pp. 293-300.
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Cranfield, CG, Cornell, BA, Grage, SL, Duckworth, P, Carne, S, Ulrich, AS & Martinac, B 2014, 'Transient Potential Gradients and Impedance Measures of Tethered Bilayer Lipid Membranes: Pore-Forming Peptide Insertion and the Effect of Electroporation', BIOPHYSICAL JOURNAL, vol. 106, no. 1, pp. 182-189.
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In this work, we present experimental data, supported by a quantitative model, on the generation and effect of potential gradients across a tethered bilayer lipid membrane (tBLM) with, to the best of our knowledge, novel architecture. A challenge to generating potential gradients across tBLMs arises from the tethering coordination chemistry requiring an inert metal such as gold, resulting in any externally applied voltage source being capacitively coupled to the tBLM. This in turn causes any potential across the tBLM assembly to decay to zero in milliseconds to seconds, depending on the level of membrane conductance. Transient voltages applied to tBLMs by pulsed or ramped direct-current amperometry can, however, provide current-voltage (I/V) data that may be used to measure the voltage dependency of the membrane conductance. We show that potential gradients >~150 mV induce membrane defects that permit the insertion of pore-forming peptides. Further, we report here the novel (to our knowledge) use of real-time modeling of conventional low-voltage alternating-current impedance spectroscopy to identify whether the conduction arising from the insertion of a polypeptide is uniform or heterogeneous on scales of nanometers to micrometers across the membrane. The utility of this tBLM architecture and these techniques is demonstrated by characterizing the resulting conduction properties of the antimicrobial peptide PGLa.

Cremona, T, Crowther, MS & Webb, JK 2014, 'Variation of prey responses to cues from a mesopredator and an apex predator', Austral Ecology, vol. 39, no. 7, pp. 749-754.
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AbstractDetection and avoidance of predator cues can be costly, so it is important for prey to balance the benefits of gaining food against the costs of avoiding predators. Balancing these factors becomes more complicated when prey are threatened by more than one type of predator. Hence, the ability to recognize species‐specific predator odours and prioritize behaviours according to the level of risk is essential for survival. We investigated how rock rats, Zyzomys spp. modify their foraging behaviour and giving‐up density (GUD) in the presence of an apex predator, the dingo Canis dingo, a mesopredator, the northern quoll Dasyurus hallucatus, a herbivore, the rock wallaby Petrogale brachyotis as a pungency control and water as a procedural control. Both dingoes and quolls consume rock rats, but because quolls can enter small crevices inhabited by rock rats, they pose a greater threat to rock rats than dingoes. Rock rats demonstrated a stronger avoidance to quoll odour than dingo odour, and no avoidance of the pungency control (rock wallaby) and the procedural control (water). GUD values declined significantly over the duration of the study, but did not differ between odour treatments. Our results support the hypothesis that prey vary behaviour according to perceived predator threat, and show stronger responses to potentially more dangerous pred...

Cun, Y, Yang, Z, Liao, J, Qiu, J, Song, Z & Yang, Y 2014, 'Enhancement of upconversion luminescence of three-dimensional ordered macroporous Bi2Ti2O7:Er3+, Yb3+ by co-doping of Li+ ions', Materials Letters, vol. 131, pp. 154-157.
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Curtis, EM, Knight, CA, Petrou, K & Leigh, A 2014, 'A comparative analysis of photosynthetic recovery from thermal stress: a desert plant case study', OECOLOGIA, vol. 175, no. 4, pp. 1051-1061.
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Our understanding of the effects of heat stress on plant photosynthesis has progressed rapidly in recent years through the use of chlorophyll a fluorescence techniques. These methods frequently involve the treatment of leaves for several hours in dark conditions to estimate declines in maximum quantum yield of photsystem II (F V/F M), rarely accounting for the recovery of effective quantum yield (ΔF/F M′) after thermally induced damage occurs. Exposure to high temperature extremes, however, can occur over minutes, rather than hours, and recent studies suggest that light influences damage recovery. Also, the current focus on agriculturally important crops may lead to assumptions about average stress responses and a poor understanding about the variation among species' thermal tolerance. We present a chlorophyll a fluorescence protocol incorporating subsaturating light to address whether species' thermal tolerance thresholds (T 50) are related to the ability to recover from short-term heat stress in 41 Australian desert species. We found that damage incurred by 15-min thermal stress events was most strongly negatively correlated with the capacity of species to recover after a stress event of 50 °C in summer. Phylogenetically independent contrast analyses revealed that basal divergences partially explain this relationship. Although T 50 and recovery capacity were positively correlated, the relationship was weaker for species with high T 50 values (>51 °C). Results highlight that, even within a single desert biome, species vary widely in their physiological response to high temperature stress and recovery metrics provide more comprehensive information than damage metrics alone. © 2014 Springer-Verlag Berlin Heidelberg.

Darling, AE, Jospin, G, Lowe, E, Matsen, FA, Bik, HM & Eisen, JA 2014, 'PhyloSift: phylogenetic analysis of genomes and metagenomes', PeerJ, vol. 2, no. 1, pp. e243-e243.
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Like all organisms on the planet, environmental microbes are subject to the forces of molecular evolution. Metagenomic sequencing provides a means to access the DNA sequence of uncultured microbes. By combining DNA sequencing of microbial communities with evolutionary modeling and phylogenetic analysis we might obtain new insights into microbiology and also provide a basis for practical tools such as forensic pathogen detection. In this work we present an approach to leverage phylogenetic analysis of metagenomic sequence data to conduct several types of analysis. First, we present a method to conduct phylogeny-driven Bayesian hypothesis tests for the presence of an organism in a sample. Second, we present a means to compare community structure across a collection of many samples and develop direct associations between the abundance of certain organisms and sample metadata. Third, we apply new tools to analyze the phylogenetic diversity of microbial communities and again demonstrate how this can be associated to sample metadata. These analyses are implemented in an open source software pipeline called PhyloSift. As a pipeline, PhyloSift incorporates several other programs including LAST, HMMER, and pplacer to automate phylogenetic analysis of protein coding and RNA sequences in metagenomic datasets generated by modern sequencing platforms (e.g., Illumina, 454). © 2014 Darling et al.

Darling, AE, McKinnon, J, Worden, P, Santos, J, Charles, IG, Chowdhury, PR & Djordjevic, SP 2014, 'A draft genome of Escherichia coli sequence type 127 strain 2009-46', GUT PATHOGENS, vol. 6, no. 1, pp. 32-32.
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© 2014 Darling et al.; licensee BioMed Central Ltd. Background: Escherichia coli are a frequent cause of urinary tract infections (UTI) and are thought to have a foodborne origin. E. coli with sequence type 127 (ST127) are emerging pathogens increasingly implicated as a cause of urinary tract infections (UTI) globally. A ST127 isolate (2009-46) resistant to ampicillin and trimethoprim was recovered from the urine of a 56 year old patient with a UTI from a hospital in Sydney, Australia and was characterised here. Results: We sequenced the genome of Escherichia coli 2009-46 using the Illumina Nextera XT and MiSeq technologies. Assembly of the sequence data reconstructed a 5.14 Mbp genome in 89 scaffolds with an N50 of 161 kbp. The genome has extensive similarity to other sequenced uropathogenic E. coli genomes, but also has several genes that are potentially related to virulence and pathogenicity that are not present in the reference E. coli strain. Conclusion: E. coli 2009-46 is a multiple antibiotic resistant, phylogroup B2 isolate recovered from a patient with a UTI. This is the first description of a drug resistant E. coli ST127 in Australia.

Darling, AE, Worden, P, Chapman, TA, Chowdhury, PR, Charles, IG & Djordjevic, SP 2014, 'The genome of Clostridium difficile 5.3', GUT PATHOGENS, vol. 6, no. 4.
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Background Clostridium difficile is the leading cause of infectious diarrhea in humans and responsible for large outbreaks of enteritis in neonatal pigs in both North America and Europe. Disease caused by C. difficile typically occurs during antibiotic therapy and its emergence over the past 40 years is linked with the widespread use of broad-spectrum antibiotics in both human and veterinary medicine. Results We sequenced the genome of Clostridium difficile 5.3 using the Illumina Nextera XT and MiSeq technologies. Assembly of the sequence data reconstructed a 4,009,318 bp genome in 27 scaffolds with an N50 of 786 kbp. The genome has extensive similarity to other sequenced C. difficile genomes, but also has several genes that are potentially related to virulence and pathogenicity that are not present in the reference C. difficile strain. Conclusion Genome sequencing of human and animal isolates is needed to understand the molecular events driving the emergence of C. difficile as a gastrointestinal pathogen of humans and food animals and to better define its zoonotic potential.

Davie, AW & Mitrovic, SM 2014, 'Benthic algal biomass and assemblage changes following environmental flow releases and unregulated tributary flows downstream of a major storage', Marine and Freshwater Research, vol. 65, no. 12, pp. 1059-1059.
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A large dam reducing the magnitude of flows regulates the Severn River, Australia. Environmental flows (EFs) are designed to increase the magnitude of flow and improve ecological outcomes such as reducing filamentous algal biomass and re-setting algal succession. The effectiveness of EF releases to alter benthic algal assemblages is poorly understood. We examined benthic algal biomass and assemblage structure at two cobble-dominated riffle sites downstream of Pindari Dam, before and after two EFs. Both EFs had discharges of ~11.6 m3 s–1 (velocity of ~0.9 m s–1). Neither EF reduced benthic algal biomass, and sometimes led to increases, with density of some filamentous algae increasing (Stigeoclonium and Leptolyngbya). An unregulated flow from a tributary between the two sites increased discharge to 25.2 m3 s–1 (velocity of ~1.2 m s–1), decreasing biomass and density of filamentous algae. The similarity in flow velocities between scouring and non-scouring events suggests that thresholds may exist and/or suspended sediments carried from unregulated tributaries may contribute to reduce algal biomass. Identifying velocities needed to reduce algal biomass are useful. Accordingly, EFs with flow velocities ~1.2 m s–1 may achieve this in river cobble-dominated riffle sections dominated by filamentous algae. Lower flow velocities of <0.9 m s–1 may result in no change or an increase in filamentous algae.

Davies, KM, Bohic, S, Carmona, A, Ortega, R, Cottam, V, Hare, DJ, Finberg, JPM, Reyes, S, Halliday, GM, Mercer, JFB & Double, KL 2014, 'Copper pathology in vulnerable brain regions in Parkinson's disease', NEUROBIOLOGY OF AGING, vol. 35, no. 4, pp. 858-866.
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Synchrotron-based x-ray fluorescence microscopy, immunofluorescence, and Western blotting were used to investigate changes in copper (Cu) and Cu-associated pathways in the vulnerable substantia nigra (SN) and locus coeruleus (LC) and in nondegenerating brain regions in cases of Parkinson’s disease (PD) and appropriate healthy and disease controls. In PD and incidental Lewy body disease, levels of Cu and Cu transporter protein 1, were significantly reduced in surviving neurons in the SN and LC. Specific activity of the cuproprotein superoxide dismutase 1 was unchanged in the SN in PD but was enhanced in the parkinsonian anterior cingulate cortex, a region with a-synuclein pathology, normal Cu, and limited cell loss. These data suggest that regions affected by a-synuclein pathology may display enhanced vulnerability and cell loss if Cu-dependent protective mechanisms are compromised. Additional investigation of copper pathology in PD may identify novel targets for the development of protective therapies for this disorder.

Davis, N, Elder, M & Reeves, L 2014, 'Non-contracting groups generated by (3,2)-automata', Algebra and Discrete Mathematics, vol. 17, no. 1, pp. 20-32.
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We add to the classification of groups generated by 3-state automata over a 2-letter alphabet given by Bondarenko et al., by showing that a number of the groups in the classification are non-contracting. We show that the criterion we use to prove a self-similar action is non-contracting also implies that the associated self-similarity graph introduced by Nekrashevych is non-hyperbolic.

de la Hunty, M, Spindler, X, Chadwick, S, Lennard, C & Roux, C 2014, 'Synthesis and application of an aqueous nile red microemulsion for the development of fingermarks on porous surfaces', FORENSIC SCIENCE INTERNATIONAL, vol. 244, pp. E48-E55.
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© 2014 Elsevier Ireland Ltd. An oil-in-water microemulsion containing a luminescent dye, nile red, has been synthesised using a solvent-diffusion method. This has been demonstrated to be effective in developing fresh latent fingermarks on porous surfaces. The working solution is made using a binary surfactant solution to create a lactescent dual organic-aqueous phase intermediate, which subsequently results in a transparent microemulsion after the organic solvent has evaporated. The solution is non-toxic and performs comparatively with a previously published methanolic formulation but at a much lower cost and with an extended shelf life. The microemulsion outperforms a previously reported aqueous nile blue formulation for the development of both charged and natural fresh fingermarks, and requires lower exposure times for image recording.

Dedousis-Wallace, A, Shute, R, Varlow, M, Murrihy, R & Kidman, T 2014, 'Predictors of teacher intervention in indirect bullying at school and outcome of a professional development presentation for teachers', Educational Psychology, vol. 34, no. 7, pp. 862-875.
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© 2013 Taylor & Francis. This study with 326 girls-school teachers developed and tested a model of predictors of the likelihood that teachers will intervene in indirect bullying, and evaluated a professional development presentation. Teachers responded to bullying vignettes before and after a presentation on indirect bullying (Experimentals) or adolescent mental health (Controls). In accord with the model, perceived seriousness of indirect bullying mediated between empathy for victims and likelihood of intervening. Self-efficacy also had a direct effect on likelihood of intervention, though level of knowledge of the impact of indirect bullying made only a small contribution. Compared with Controls, the Experimental Group scored more highly, after the presentation, on perceived seriousness of indirect bullying, empathy for victims, likelihood of intervening and self-efficacy, but not on knowledge of impact. It is concluded that teacher education about indirect bullying may be most effective if it focuses on feelings rather than facts, and provides practical intervention strategies.

Dinamarca, MA, Rojas, A, Baeza, P, Espinoza, G, Ibacache-Quiroga, C & Ojeda, J 2014, 'Optimizing the biodesulfurization of gas oil by adding surfactants to immobilized cell systems', Fuel, vol. 116, pp. 237-241.
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DIXON-BRIDGES, K, GLADSTONE, W & HUTCHINGS, PAT 2014, 'One new species of Micronephthys Friedrich, 1939 and one new species of <br />Nephtys Cuvier, 1817 (Polychaeta: Phyllodocida: Nephtyidae) <br />from eastern Australia with notes on Aglaophamus australiensis (Fauchald, 1965) and a key to all Australian species', Zootaxa, vol. 3872, no. 5, pp. 513-513.
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There are currently over 130 described species of Nephtyidae worldwide, with 18 species known from Australian waters belonging to four genera. Two new species are described, Micronephthys derupeli n. sp., and Nephtys triangula n. sp., from Eastern Australia. Descriptions are provided for all species examined. Comments are given about the recent transfer of Nephtys australiensis to Aglaophamus. A key to all Australian species of nephtyids is provided. 

Dixon-Bridges, K, Hutchings, P & Gladstone, W 2014, 'Effectiveness of habitat classes as surrogates for biodiversity in marine reserve planning', AQUATIC CONSERVATION-MARINE AND FRESHWATER ECOSYSTEMS, vol. 24, no. 4, pp. 463-477.
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1. Surrogates are used in marine conservation planning when there is limited information on the distribution of biodiversity, and representation of species and assemblage diversity are conservation goals. With prior confirmation of their relationship to spatial variation in biodiversity, habitat classification schemes are a potentially useful surrogate. 2. Polychaetes can comprise over one-third of species of benthic infaunal assemblages, they are the most frequent and abundant marine metazoans in benthic environments, and they are a reliable surrogate for other macrobenthic taxa. 3. It was tested whether polychaete biodiversity differed among six estuarine habitat classes defined for conservation planning in the Port StephensGreat Lakes Marine Park, New South Wales, Australia: subtidal sand, mud, muddy sand, and seagrass beds comprising Posidonia australis, Zostera capricorni and mixed Posidonia/Zostera. Polychaetes were sampled from replicate sites in each habitat and differences among habitat classes in species richness, abundance, and assemblage structure were examined. Several environmental variables, known to be important determinants of polychaete distribution, were also quantified at each site. 4. Ninety-five species of polychaetes (belonging to 35 families) were identified. Species richness and abundance did not differ among the habitat classes. Polychaete assemblages of subtidal sand differed from assemblages in both mud and muddy sand, however, assemblages in all other habitats were not different. A combination of some of the measured environmental variables (distance to the estuary entrance, depth, sediment grain size) was a more important determinant of assemblage variation than the habitat classes. 5. Using these predictors, an alternative habitat classification scheme to the scheme currently utilized in marine park planning is proposed. 6. This study demonstrates the critical importance of testing assumptions about surrogacy and an approach for ref...

Donati, M, Huot-Creasy, H, Humphrys, M, Di Paolo, M, Di Francesco, A & Myers, GSA 2014, 'Genome Sequence of Chlamydia suis MD56, Isolated from the Conjunctiva of a Weaned Piglet', Genome Announcements, vol. 2, no. 3, pp. e00425-14-e00425-14.
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ABSTRACT Chlamydia suis is a natural pathogen of pigs ( Sus scrofa ) and causes conjunctivitis, pneumonia, enteritis, and various reproductive disorders that adversely impact this economically important animal. Here, we report the first C. suis genome, that of C. suis MD56, isolated from a conjunctival swab of a weaned piglet.

Donelson, JM, McCormick, MI, Booth, DJ & Munday, PL 2014, 'Reproductive Acclimation to Increased Water Temperature in a Tropical Reef Fish', PLOS ONE, vol. 9, no. 5, pp. 1-9.
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Understanding the capacity of organisms to cope with projected global warming through acclimation and adaptation is critical to predicting their likely future persistence. While recent research has shown that developmental acclimation of metabolic attributes to ocean warming is possible, our understanding of the plasticity of key fitness-associated traits, such as reproductive performance, is lacking. We show that while the reproductive ability of a tropical reef fish is highly sensitive to increases in water temperature, reproductive capacity at +1.5°C above present-day was improved to match fish maintained at present-day temperatures when fish complete their development at the higher temperature. However, reproductive acclimation was not observed in fish reared at +3.0°C warmer than present-day, suggesting limitations to the acclimation possible within one generation. Surprisingly, the improvements seen in reproduction were not predicted by the oxygen- and capacity-limited thermal tolerance hypothesis. Specifically, pairs reared at +1.5°C, which showed the greatest capacity for reproductive acclimation, exhibited no acclimation of metabolic attributes. Conversely, pairs reared at +3.0°C, which exhibited acclimation in resting metabolic rate, demonstrated little capacity for reproductive acclimation. Our study suggests that understanding the acclimation capacity of reproductive performance will be critically important to predicting the impacts of climate change on biological systems. © 2014 Donelson et al.

Donley, C, McClelland, K, McKeen, HD, Nelson, L, Yakkundi, A, Jithesh, PV, Burrows, J, McClements, L, Valentine, A, Prise, KM, McCarthy, HO & Robson, T 2014, 'Identification of RBCK1 as a novel regulator of FKBPL: implications for tumor growth and response to tamoxifen', Oncogene, vol. 33, no. 26, pp. 3441-3450.
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Donnelly, JL, Sturmberg, BCP, Dossou, KB, Botten, LC, Asatryan, AA, Poulton, CG, McPhedran, RC & de Sterke, CM 2014, 'Mode-based analysis of silicon nanohole arrays for photovoltaic applications', OPTICS EXPRESS, vol. 22, no. 17, pp. A1343-A1354.
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We investigate the optical properties of silicon nanohole arrays for application in photovoltaic cells in terms of the modes within the structure. We highlight three types of modes: fundamental modes, important at long wavelengths; guided resonance modes, which enhance absorption for wavelengths where the intrinsic absorption of silicon is low; and channeling modes, which suppress front-surface reflection. We use this understanding to explain why the parameters of optimized nanohole arrays occur in specific ranges even as the thickness is varied. © 2014 Optical Society of America.

Donovan, C, Simoons, M, Esposito, J, Cheong, JN, FitzPatrick, M & Bourke, JE 2014, 'Rosiglitazone is a superior bronchodilator compared to chloroquine and beta-adrenoceptor agonists in mouse lung slices', RESPIRATORY RESEARCH, vol. 15.
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Dooley, AH, Golodets, VY & Zhang, G 2014, 'Sub-additive ergodic theorems for countable amenable groups', JOURNAL OF FUNCTIONAL ANALYSIS, vol. 267, no. 5, pp. 1291-1320.
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In this paper we generalize Kingman's sub-additive ergodic theorem to a large class of infinite countable discrete amenable group actions. © 2014 Elsevier Inc.

Dowd, A, Pissuwan, D & Cortie, MB 2014, 'Optical readout of the intracellular environment using nanoparticle transducers', TRENDS IN BIOTECHNOLOGY, vol. 32, no. 11, pp. 571-577.
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Dowton, M, Meiklejohn, K, Cameron, SL & Wallman, J 2014, 'A Preliminary Framework for DNA Barcoding, Incorporating the Multispecies Coalescent', Systematic Biology, vol. 63, no. 4, pp. 639-644.
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Dugan, VG, Emrich, SJ, Giraldo-Calderón, GI, Harb, OS, Newman, RM, Pickett, BE, Schriml, LM, Stockwell, TB, Stoeckert, CJ, Sullivan, DE, Singh, I, Ward, DV, Yao, A, Zheng, J, Barrett, T, Birren, B, Brinkac, L, Bruno, VM, Caler, E, Chapman, S, Collins, FH, Cuomo, CA, Di Francesco, V, Durkin, S, Eppinger, M, Feldgarden, M, Fraser, C, Fricke, WF, Giovanni, M, Henn, MR, Hine, E, Hotopp, JD, Karsch-Mizrachi, I, Kissinger, JC, Lee, EM, Mathur, P, Mongodin, EF, Murphy, CI, Myers, G, Neafsey, DE, Nelson, KE, Nierman, WC, Puzak, J, Rasko, D, Roos, DS, Sadzewicz, L, Silva, JC, Sobral, B, Squires, RB, Stevens, RL, Tallon, L, Tettelin, H, Wentworth, D, White, O, Will, R, Wortman, J, Zhang, Y & Scheuermann, RH 2014, 'Standardized Metadata for Human Pathogen/Vector Genomic Sequences', PLoS ONE, vol. 9, no. 6, pp. e99979-e99979.
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High throughput sequencing has accelerated the determination of genome sequences for thousands of human infectious disease pathogens and dozens of their vectors. The scale and scope of these data are enabling genotype-phenotype association studies to identify genetic determinants of pathogen virulence and drug/insecticide resistance, and phylogenetic studies to track the origin and spread of disease outbreaks. To maximize the utility of genomic sequences for these purposes, it is essential that metadata about the pathogen/vector isolate characteristics be collected and made available in organized, clear, and consistent formats. Here we report the development of the GSCID/BRC Project and Sample Application Standard, developed by representatives of the Genome Sequencing Centers for Infectious Diseases (GSCIDs), the Bioinformatics Resource Centers (BRCs) for Infectious Diseases, and the U.S. National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health (NIH), informed by interactions with numerous collaborating scientists. It includes mapping to terms from other data standards initiatives, including the Genomic Standards Consortium's minimal information (MIxS) and NCBI's BioSample/BioProjects checklists and the Ontology for Biomedical Investigations (OBI). The standard includes data fields about characteristics of the organism or environmental source of the specimen, spatial-temporal information about the specimen isolation event, phenotypic characteristics of the pathogen/vector isolated, and project leadership and support. By modeling metadata fields into an ontology-based semantic framework and reusing existing ontologies and minimum information checklists, the application standard can be extended to support additional project-specific data fields and integrated with other data represented with comparable standards. The use of this metadata standard by all ongoing and future GSCID sequencing projects will provide a consi...

Duursma, RA, Barton, CVM, Lin, Y-S, Medlyn, BE, Eamus, D, Tissue, DT, Ellsworth, DS & McMurtrie, RE 2014, 'The peaked response of transpiration rate to vapour pressure deficit in field conditions can be explained by the temperature optimum of photosynthesis', AGRICULTURAL AND FOREST METEOROLOGY, vol. 189, pp. 2-10.
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Dyari, HRE, Rawling, T, Bourget, K & Murray, M 2014, 'Synthetic ω-3 Epoxyfatty Acids As Antiproliferative and Pro-apoptotic Agents in Human Breast Cancer Cells', Journal of Medicinal Chemistry, vol. 57, no. 17, pp. 7459-7464.
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Eamens, AL, Smith, NA, Dennis, ES, Wassenegger, M & Wang, M-B 2014, 'In Nicotiana species, an artificial microRNA corresponding to the virulence modulating region of Potato spindle tuber viroid directs RNA silencing of a soluble inorganic pyrophosphatase gene and the development of abnormal phenotypes', VIROLOGY, vol. 450, pp. 266-277.
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Potato spindle tuber viroid (PSTVd) is a small non-protein-coding RNA pathogen that can induce disease symptoms in a variety of plant species. How PSTVd induces disease symptoms is a long standing question. It has been suggested that PSTVd-derived small RNAs (sRNAs) could direct RNA silencing of a targeted host gene(s) resulting in symptom development. To test this, we expressed PSTVd sequences as artificial microRNAs (amiRNAs) in Nicotiana tabacum and Nicotiana benthamiana. One amiRNA, amiR46 that corresponds to sequences within the PSTVd virulence modulating region (VMR), induced abnormal phenotypes in both Nicotiana species that closely resemble those displayed by PSTVd infected plants. In N. tabacum amiR46 plants, phenotype severity correlated with amiR46 accumulation and expression down-regulation of the bioinformatically-identified target gene, a Nicotiana soluble inorganic pyrophosphatase (siPPase). Taken together, our phenotypic and molecular analyses suggest that disease symptom development in Nicotiana species following PSTVd infection results from sRNA-directed RNA silencing of the host gene, siPPase.

Earl, D, Nguyen, N, Hickey, G, Harris, RS, Fitzgerald, S, Beal, K, Seledtsov, I, Molodtsov, V, Raney, BJ, Clawson, H, Kim, J, Kemena, C, Chang, J-M, Erb, I, Poliakov, A, Hou, M, Herrero, J, Kent, WJ, Solovyev, V, Darling, AE, Ma, J, Notredame, C, Brudno, M, Dubchak, I, Haussler, D & Paten, B 2014, 'Alignathon: a competitive assessment of whole-genome alignment methods', Genome Research, vol. 24, no. 12, pp. 2077-2089.
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Multiple sequence alignments (MSAs) are a prerequisite for a wide variety of evolutionary analyses. Published assessments and benchmark data sets for protein and, to a lesser extent, global nucleotide MSAs are available, but less effort has been made to establish benchmarks in the more general problem of whole-genome alignment (WGA). Using the same model as the successful Assemblathon competitions, we organized a competitive evaluation in which teams submitted their alignments and then assessments were performed collectively after all the submissions were received. Three data sets were used: Two were simulated and based on primate and mammalian phylogenies, and one was comprised of 20 real fly genomes. In total, 35 submissions were assessed, submitted by 10 teams using 12 different alignment pipelines. We found agreement between independent simulation-based and statistical assessments, indicating that there are substantial accuracy differences between contemporary alignment tools. We saw considerable differences in the alignment quality of differently annotated regions and found that few tools aligned the duplications analyzed. We found that many tools worked well at shorter evolutionary distances, but fewer performed competitively at longer distances. We provide all data sets, submissions, and assessment programs for further study and provide, as a resource for future benchmarking, a convenient repository of code and data for reproducing the simulation assessments.

El Ridi, R, Tallima, H, Dalton, JP & Donnelly, S 2014, 'Induction of protective immune responses against schistosomiasis using functionally active cysteine peptidases', FRONTIERS IN GENETICS, vol. 5, no. MAY.
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Each year schistosomiasis afflicts up to 600 million people in 74 tropical and sub-tropical countries, predominantly in the developing world. Yet we depend on a single drug, praziquantel, for its treatment and control. There is no vaccine available but one is urgently needed especially since praziquantel-resistant parasites are likely to emerge at some time in the future. The disease is caused by several worm species of the genus Schistosoma. These express several classes of papain-like cysteine peptidases, cathepsins B and L, in various tissues but particularly in their gastrodermis where they employ them as digestive enzymes. We have shown that sub-cutaneous injection of recombinant and functionally active Schistosoma mansoni cathepsin B1 (SmCB1), or a cathepsin L from a related parasite Fasciola hepatica (FhCL1), elicits highly significant protection (up to 73%) against an experimental challenge worm infection in murine models of schistosomiasis. The immune modulating properties of this subcutaneous injection can boost protection levels (up to 83%) when combined with other S. mansoni vaccine candidates, glyceraldehyde 3-phosphate dehydrogenase (SG3PDH) and peroxiredoxin (PRX-MAP). Here, we discuss these data in the context of the parasite's biology and development, and provide putative mechanism by which the native-like cysteine peptidase induce protective immune responses. © 2014 El Ridi, Tallima, Dalton and Donnelly.

El Ridi, R, Tallima, H, Selim, S, Donnelly, S, Cotton, S, Santana, BG & Dalton, JP 2014, 'Cysteine Peptidases as Schistosomiasis Vaccines with Inbuilt Adjuvanticity', PLOS ONE, vol. 9, no. 1.
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Schistosomiasis is caused by several worm species of the genus Schistosoma and afflicts up to 600 million people in 74 tropical and sub-tropical countries in the developing world. Present disease control depends on treatment with the only available drug praziquantel. No vaccine exists despite the intense search for molecular candidates and adjuvant formulations over the last three decades. Cysteine peptidases such as papain and Der p 1 are well known environmental allergens that sensitize the immune system driving potent Th2-responses. Recently, we showed that the administration of active papain to mice induced significant protection (P<0.02, 50%) against an experimental challenge infection with Schistosoma mansoni. Since schistosomes express and secrete papain-like cysteine peptidases we reasoned that these could be employed as vaccines with inbuilt adjuvanticity to protect against these parasites. Here we demonstrate that subcutaneous injection of functionally active S. mansoni cathepsin B1 (SmCB1), or a cathepsin L from a related parasite Fasciola hepatica (FhCL1), elicits highly significant (P<0.0001) protection (up to 73%) against an experimental challenge worm infection. Protection and reduction in worm egg burden were further increased (up to 83%) when the cysteine peptidases were combined with other S. mansoni vaccine candidates, glyceraldehyde 3-phosphate dehydrogenase (SG3PDH) and peroxiredoxin (PRX-MAP), without the need to add chemical adjuvants. These studies demonstrate the capacity of helminth cysteine peptidases to behave simultaneously as immunogens and adjuvants, and offer an innovative approach towards developing schistosomiasis vaccines. © 2014 El Ridi et al.

El Saliby, I, Erdei, L, McDonagh, A, Kim, J-B, Kim, J-H & Shon, HK 2014, 'Co-doped mesoporous titania photocatalysts prepared from a peroxo-titanium complex solution', MATERIALS RESEARCH BULLETIN, vol. 49, pp. 7-13.
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In this study, nitrogen doped and nitrogen/silver co-doped TiO2 photocatalsysts were fabricated using a sol–gel method at room temperature. The obtained gels were neutralized, washed with pure water, and calcined at 400 °C for 4 h. The photocatalysts were characterized by scanning and transmission electron microscopy, X-ray diffraction, diffuse reflectance spectroscopy, X-ray photoelectron spectroscopy, and BET specific surface area. The results showed that spherical particles with anatase structure were produced after annealing at 400 °C. N 1s (400 eV) and Ag 3d (367.3 eV) states indicated that nitrogen doping and silver co-doping were in the form of NO bonds and AgO, respectively. The photocatalytic activity of photocatalysts was investigated using a batch reactor system exposed to artificial solar irradiation. Both nitrogen and silver/nitrogen co-doped materials were effective in the photocatalytic degradation of hexamethyl pararosaniline chloride.

El-Assaad, F, Combes, V & Grau, GE 2014, 'Experimental Models of Microvascular Immunopathology: The Example of Cerebral Malaria.', J Neuroinfect Dis, vol. 5, no. 1, pp. 1-11.
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Human cerebral malaria is a severe and often lethal complication of Plasmodium falciparum infection. Complex host and parasite interactions should the precise mechanisms involved in the onset of this neuropathology. Adhesion of parasitised red blood cells and host cells to endothelial cells lead to profound endothelial alterations that trigger immunopathological changes, varying degrees of brain oedema and can compromise cerebral blood flow, cause cranial nerve dysfunction and hypoxia. Study of the cerebral pathology in human patients is limited to clinical and genetic field studies in endemic areas, thus cerebral malaria (CM) research relies heavily on experimental models. The availability of malaria models allows study from the inoculation of Plasmodium to the onset of disease and permit invasive experiments. Here, we discuss some aspects of our current understanding of CM, the experimental models available and some important recent findings extrapolated from these models.

El-Assaad, F, Combes, V, Grau, GER & Jambou, R 2014, 'Potential Efficacy of Citicoline as Adjunct Therapy in Treatment of Cerebral Malaria', Antimicrobial Agents and Chemotherapy, vol. 58, no. 1, pp. 602-605.
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ABSTRACT Cerebral malaria (CM) is characterized by a dysregulated immune response that results in endothelial membrane destabilization and increased microparticle (MP) production. Citicoline (CTC) is a membrane stabilizer used for the treatment of neurological disorders. We evaluated the efficacy of CTC as adjunct therapy to aid recovery from experimental CM. We show that CTC reduces MP production in vitro ; in combination with artesunate in vivo , confers partial protection against CM; and prolongs survival.

El-Assaad, F, Wheway, J, Hunt, NH, Grau, GER & Combes, V 2014, 'Production, Fate and Pathogenicity of Plasma Microparticles in Murine Cerebral Malaria', PLoS Pathogens, vol. 10, no. 3, pp. e1003839-e1003839.
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In patients with cerebral malaria (CM), higher levels of cell-specific microparticles (MP) correlate with the presence of neurological symptoms. MP are submicron plasma membrane-derived vesicles that express antigens of their cell of origin and phosphatidylserine (PS) on their surface, facilitating their role in coagulation, inflammation and cell adhesion. In this study, the in vivo production, fate and pathogenicity of cell-specific MP during Plasmodium berghei infection of mice were evaluated. Using annexin V, a PS ligand, and flow cytometry, analysis of platelet-free plasma from infected mice with cerebral involvement showed a peak of MP levels at the time of the neurological onset. Phenotypic analyses showed that MP from infected mice were predominantly of platelet, endothelial and erythrocytic origins. To determine the in vivo fate of MP, we adoptively transferred fluorescently labelled MP from mice with CM into healthy or infected recipient mice. MP were quickly cleared following intravenous injection, but microscopic examination revealed arrested MP lining the endothelium of brain vessels of infected, but not healthy, recipient mice. To determine the pathogenicity of MP, we transferred MP from activated endothelial cells into healthy recipient mice and this induced CM-like brain and lung pathology. This study supports a pathogenic role for MP in the aggravation of the neurological lesion and suggests a causal relationship between MP and the development of CM. © 2014 El-Assaad et al.

Elcombe, MM, Kealley, CS, Bhatia, VK, Thorogood, GJ, Carter, DJ, Avdeev, M & Cortie, MB 2014, 'Determination of martensite structures of the Au7Cu5Al4 and Au7Cu5.7Al3.3 shape-memory alloys', ACTA MATERIALIA, vol. 79, pp. 234-240.
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The β-phase of Au 7 Cu 5 Al 4 undergoes a reversible shape-memory phase transformation for which several conflicting martensite phases have been reported. Here we show the significance of the cooling temperature used to obtain the martensite. If Au 7 Cu 5 Al 4 is cooled from the parent phase condition to cryogenic temperatures, e.g. below 200 K, the martensitic phase is orthorhombic (space group Pcmn, a = 4.4841 Å, b = 5.8996 Å, c = 17.8130 Å); however, when this composition is cooled to only ∼260 K it will in general consist of a mixture of orthorhombic and monoclinic phase (the latter has space group P2 1 /m, a = 4.4742 Å, b = 5.9265 Å, c = 13.3370 Å, β = 91.425°). In contrast, a sample with decreased Al content (Au 7 Cu 5.7 Al 3.3 ) transforms fully to monoclinic phase if cooled to ∼260 K. © 2014 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Elder, M & Hermiller, S 2014, 'Minimal Almost Convexity', Journal of Group Theory, vol. 8, no. 2, pp. 239-266.
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In this article we show that the Baumslag-Solitar group $BS(1,2)$ isminimally almost convex, or $MAC$. We also show that $BS(1,2)$ does not satisfyPo\'enaru's almost convexity condition $P(2)$, and hence the condition $P(2)$is strictly stronger than $MAC$. Finally, we show that the groups $BS(1,q)$ for$q \geq 7$ and Stallings' non-$FP_3$ group do not satisfy $MAC$. As aconsequence, the condition $MAC$ is not a commensurability invariant.

Elder, M, Lee, G & Rechnitzer, A 2014, 'Permutations generated by a depth 2 and infinite stack in series are algebraic', Electronic Journal of Combinatorics, vol. 22, pp. Paper 2.16-23.
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We prove that the class of permutations generated by passing an orderedsequence $12\dots n$ through a stack of depth 2 and an infinite stack in seriesis in bijection with an unambiguous context-free language, where a permutationof length $n$ is encoded by a string of length $3n$. It follows that thesequence counting the number of permutations of each length has an algebraicgenerating function. We use the explicit context-free language to compute thegenerating function: \begin{align*} \sum_{n\geq 0} c_n t^n &=\frac{(1+q)\left(1+5q-q^2-q^3-(1-q)\sqrt{(1-q^2)(1-4q-q^2)}\right)}{8q}\end{align*} where $c_n$ is the number of permutations of length $n$ that canbe generated, and $q \equiv q(t) = \frac{1-2t-\sqrt{1-4t}}{2t}$ is a simplevariant of the Catalan generating function. This in turn implies that$c_n^{1/n} \to 2+2\sqrt{5}$.

Elder, M, Rechnitzer, A, van Rensburg, EJJ & Wong, T 2014, 'The cogrowth series for BS(N, N) is D-finite', INTERNATIONAL JOURNAL OF ALGEBRA AND COMPUTATION, vol. 24, no. 2, pp. 171-187.
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We compute the cogrowth series for Baumslag-Solitar groups BS(N, N) = (a,b aNb = baN), which we show to be D-finite. It follows that their cogrowth rates are algebraic numbers. © 2014 World Scientific Publishing Company.

Elliott, R, Rai, T & McKinley, S 2014, 'Factors affecting sleep in the critically ill: An observational study', JOURNAL OF CRITICAL CARE, vol. 29, no. 5, pp. 859-863.
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Purpose: The aims of the current study were to describe the extrinsic and intrinsic factors affecting sleep in critically ill patients and to examine potential relationships with sleep quality. Materials and Methods: Sleep was recorded using polysomnography (PSG) and self-reports collected in adult patients in intensive care. Sound and illuminance levels were recorded during sleep recording. Objective sleep quality was quantified using total sleep time divided by the number of sleep periods (PSG sleep period time ratio). A regression model was specified using the 'PSG sleep period time ratio' as a dependent variable. Results: Sleep was highly fragmented. Patients rated noise and light as the most sleep disruptive. Continuous equivalent sound levels were 56 dB (A). Median daytime illuminance level was 74 lux, and nighttime levels were 1 lux. The regression model explained 25% of the variance in sleep quality (P = .027); the presence of an artificial airway was the only statistically significant predictor in the model (P = .007). Conclusions: The presence of an artificial airway during sleep monitoring was the only significant predictor in the regression model and may suggest that although potentially uncomfortable, an artificial airway may actually promote sleep. This requires further investigation. © 2014 Elsevier Inc.

Everett, JD, Baird, ME, Roughan, M, Suthers, IM & Doblin, MA 2014, 'Relative impact of seasonal and oceanographic drivers on surface chlorophyll a along a Western Boundary Current', PROGRESS IN OCEANOGRAPHY, vol. 120, pp. 340-351.
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Strengthening Western Boundary Currents (WBCs) advect warm, low nutrient waters into temperate latitudes, displacing more productive waters. WBCs also influence phytoplankton distribution and growth through current-induced upwelling, mesoscale eddy intrusion and seasonal changes in strength and poleward penetration. Here we examine dynamics of chlorophyll a (Chl. a) in the western Pacific Ocean, a region strongly influenced by the East Australian Current (EAC). We interpreted a spatial and temporal analysis of satellite-derived surface Chl. a, using a hydrodynamic model, a wind-reanalysis product and an altimetry-derived eddy-census. Our analysis revealed regions of persistently elevated surface Chl. a along the continental shelf and showed that different processes have a dominant effect in different locations. In the northern and central zones, upwelling events tend to regulate surface Chl. a patterns, with peaks in phytoplankton biomass corresponding to two known upwelling locations south of Cape Byron (28.5S) and Smoky Cape (31S). Within the central EAC separation zone, positive surface Chl. a anomalies occurred 65% of the time when both wind-stress (sw) and bottom-stress (sB) were upwelling- favourable, and only 17% of the time when both were downwelling-favourable. The interaction of wind and the EAC was a critical driver of surface Chl. a dynamics, with upwelling-favourable sW resulting in a 70% increase in surface Chl. a at some locations, when compared to downwelling-favourable sW. In the southern zone, surface Chl. a was driven by a strong seasonal cycle, with phytoplankton biomass increasing up to 152% annually each spring. The Stockton Bight region (32.2533.25S) contained P20% of the total shelf Chl. a on 27% of occasions due to its location downstream of upwelling locations, wide shelf area and reduced surface velocities. This region is analogous to productive fisheries regions in the Aghulus Current (Natal Bight) and Kuroshio Current (Enshu-nada Sea)...

Fair, KM, Arnold, MD & Ford, MJ 2014, 'Determination of the elastic properties of graphene by indentation and the validity of classical models of indentation', JOURNAL OF PHYSICS-CONDENSED MATTER, vol. 26, no. 1, pp. 1-8.
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Ab initio and empirical force field methods are used to simulate the loading of a large graphene membrane under an indenter analogous to an atomic force microscope tip. From these calculations we attempt to resolve ambiguities around determination of the elastic constants of graphene from such indentation experiments. We investigate the effect of the formation of wrinkles and more importantly the applicability of modelling the membrane as a continuous elastic sheet. By comparing empirical potential and large scale density functional theory calculations we have also assessed the performance of classical potentials in describing bending in this system. We find that the in-plane Young's modulus deduced from the indentation simulations using the classical expression for a clamped elastic membrane under a central point load is not consistent with that calculated directly from the in-plane stress-strain curve. © 2014 IOP Publishing Ltd.

Faiz, A, Tjin, G, Harkness, L, Weckmann, M, Bao, S, Black, JL, Oliver, BGG & Burgess, JK 2014, 'Correction: The Expression and Activity of Cathepsins D, H and K in Asthmatic Airways', PLoS ONE, vol. 9, no. 1.
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Farrell, H, Gentien, P, Fernand, L, Lazure, P, Lunven, M, Youenou, A, Reguera, B & Raine, R 2014, 'Vertical and horizontal controls of a haptophyte thin layer in the Bay of Biscay, France', DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY, vol. 101, pp. 80-94.
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Investigations into the phytoplankton of the Bay of Biscay in July 2006 revealed an extensive bloom of an unidentified haptophyte species. High-resolution sampling techniques identified the region in the vicinity of the mouth of the Loire estuary as an area of high (10 6 -10 7 cellsl -1 ) cell densities of the haptophyte in a thin sub-surface layer. This organism dominated the phytoplankton population regionally. Measurements of the vertical distribution of horizontal shear showed that the population, located at ca. 20m depth, was confined to a layer lying between two density discontinuities with high shear. Physical measurements indicated that the population was being advected southeastwards, along the coast. Seaward spreading of the population was also noted during the survey. Horizontal diffusion could be derived from the changes in the offshore gradient in the population's distribution with time, with estimates of Kx, the horizontal diffusion coefficient, of the order of 100m 2 s -1 . The magnitude of horizontal dispersion is compared with that of horizontal advective flux, vertical dispersion and growth. © 2013 Elsevier Ltd.

Farrell, H, Velo-Suarez, L, Reguera, B & Raine, R 2014, 'Phased cell division, specific division rates and other biological observations of Dinophysis populations in sub-surface layers off the south coast of Ireland', DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY, vol. 101, pp. 249-254.
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The proportions of viable cells of Dinophysis spp. that were paired (dividing) and recently divided during a cell cycle were measured on populations of D. acuta and D. acuminata observed off the south coast of Ireland in July 2007 and July 2009. Both species exhibited phased cell division in 2009 with maximum frequency of division (f max ) 2h after sunrise. Different patterns of division (timing of f max ) were shown by D. acuta in 2007, when the population aggregated in a thin layer was transported by a coastal jet flow. High resolution (decimetre-scale) profiles within the thin layer showed large differences in the vertical distribution of biological properties (feeding status, mortality). Values of the specific growth rate μ were compared to estimates derived in similar fashion from observations on Dinophysis populations elsewhere. Different patterns exhibited by the same species in different regions may be attributed to adaptations to latitudinal differences (length of photoperiod). The question of whether phased cell division always occurs in Dinophysis populations, and the incorporation of the potential specific division rate into models of Dinophysis growth are discussed. Comprehensive field data sets demonstrate the impact of the results on the coherence of Dinophysis populations during their transport along the Irish coast in jet-like flows towards sites of intensive shellfish culture. © 2013 Elsevier Ltd.

Favaloro, J, Liyadipitiya, T, Brown, R, Yang, S, Suen, H, Woodland, N, Nassif, N, Hart, D, Fromm, P, Weatherburn, C, Gibson, J, Ho, PJ & Joshua, D 2014, 'Myeloid derived suppressor cells are numerically, functionally and phenotypically different in patients with multiple myeloma', LEUKEMIA & LYMPHOMA, vol. 55, no. 12, pp. 2893-2900.
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© 2014 Informa UK, Ltd. Myeloid derived suppressor cells (MDSCs) are a heterogeneous population of cells that have been implicated as inhibitors of lymphopoiesis in patients with malignancies. They have a consensus phenotype of CD33+/CD11b+/HLA-DRlo/-and can be further divided into CD15 + granulocytic (G-MDSC) and CD14 + monocytic (M-MDSC) subsets. We characterized MDSCs in patients with multiple myeloma (MM) and found a significant increase in G-MDSCs in the blood of patients with progressive MM. Flow-sorted MDSCs from patients with MM induced the generation of regulatory T cells (Treg). MDSCs from both patients with MM and aged-matched controls demonstrated a dose-dependent inhibition of lymphocyte proliferation in carboxyfluorescein succinimidyl ester (CFSE)-tracking experiments. Granulocyte colony stimulating factor (G-CSF) administered to induce stem cell mobilization caused an increase in the number of MDSCs in the peripheral blood of patients with MM and a concentration of these immune-suppressive cells in peripheral blood stem cell collections. MDSCs are likely to cause immune dysfunction in patients with MM.

Feary, DA, Fowler, AM & Ward, TJ 2014, 'Developing a rapid method for undertaking the World Ocean Assessment in data-poor regions - A case study using the South China Sea Large Marine Ecosystem', OCEAN & COASTAL MANAGEMENT, vol. 95, pp. 129-137.
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Feary, DA, Pratchett, MS, Emslie, MJ, Fowler, AM, Figueira, WF, Luiz, OJ, Nakamura, Y & Booth, DJ 2014, 'Latitudinal shifts in coral reef fishes: why some species do and others do not shift', FISH AND FISHERIES, vol. 15, no. 4, pp. 593-615.
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© 2013 John Wiley & Sons Ltd. Climate change is resulting in rapid poleward shifts in the geographical distribution of many tropical fish species, but it is equally apparent that some fishes are failing to exhibit expected shifts in their geographical distribution. There is still little understanding of the species-specific traits that may constrain or promote successful establishment of populations in temperate regions. We review the factors likely to affect population establishment, including larval supply, settlement and post-settlement processes. In addition, we conduct meta-analyses on existing and new data to examine relationships between species-specific traits and vagrancy. We show that tropical vagrant species are more likely to originate from high-latitude populations, while at the demographic level, tropical fish species with large body size, high swimming ability, large size at settlement and pelagic spawning behaviour are more likely to show successful settlement into temperate habitats. We also show that both habitat and food limitation at settlement and within juvenile stages may constrain tropical vagrant communities to those species with medium to low reliance on coral resources.

Fierro, AO & Leslie, LM 2014, 'Relationships between Southeast Australian Temperature Anomalies and Large-Scale Climate Drivers', Journal of Climate, vol. 27, no. 4, pp. 1395-1412.
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Abstract Over the past century, particularly after the 1960s, observations of mean maximum temperatures reveal an increasing trend over the southeastern quadrant of the Australian continent. Correlation analysis of seasonally averaged mean maximum temperature anomaly data for the period 1958–2012 is carried out for a representative group of 10 stations in southeast Australia (SEAUS). For the warm season (November–April) there is a positive relationship with the El Niño–Southern Oscillation (ENSO) and the Pacific decadal oscillation (PDO) and an inverse relationship with the Antarctic Oscillation (AAO) for most stations. For the cool season (May–October), most stations exhibit similar relationships with the AAO, positive correlations with the dipole mode index (DMI), and marginal inverse relationships with the Southern Oscillation index (SOI) and the PDO. However, for both seasons, the blocking index (BI, as defined by M. Pook and T. Gibson) in the Tasman Sea (160°E) clearly is the dominant climate mode affecting maximum temperature variability in SEAUS with negative correlations in the range from r = −0.30 to −0.65. These strong negative correlations arise from the usual definition of BI, which is positive when blocking high pressure systems occur over the Tasman Sea (near 45°S, 160°E), favoring the advection of modified cooler, higher-latitude maritime air over SEAUS. A point-by-point correlation with global sea surface temperatures (SSTs), principal component analysis, and wavelet power spectra support the relationships with ENSO and DMI. Notably, the analysis reveals that the maximum temperature variability of one group of stations is explained primarily by local factors (warmer near-coastal SSTs), rather than teleconnections with large-scale drivers.

Fletcher, S, Caprarelli, G, Merif, J, Andresen, D, Hal, SV, Stark, D & Ellis, J 2014, 'Epidemiology and Geographical Distribution of Enteric Protozoan Infections in Sydney, Australia', Journal of Public Health Research, vol. 3, no. 2, pp. jphr.2014.298-jphr.2014.298.
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Background Enteric protozoa are associated with diarrhoeal illnesses in humans; however there are no recent studies on their epidemiology and geographical distribution in Australia. This study describes the epidemiology of enteric protozoa in the state of New South Wales and incorporates spatial analysis to describe their distribution. Design and methods Laboratory and clinical records from four public hospitals in Sydney for 910 patients, who tested positive for enteric protozoa over the period January 2007 - December 2010, were identified, examined and analysed. We selected 580 cases which had residence post code data available, enabling us to examine the geographic distribution of patients, and reviewed the clinical data of 252 patients to examine possible links between protozoa, demographic and clinical features. Results Frequently detected protozoa were Blastocystis spp. (57%), Giardia intestinalis (27%) and Dientamoeba fragilis (12%). The age distribution showed that the prevalence of protozoa decreased with age up to 24 years but increasing with age from 25 years onwards. The geographic provenance of the patients indicates that the majority of cases of Blastocystis (53.1%) are clustered in and around the Sydney City Business District, while pockets of giardiasis were identified in regional/rural areas. The distribution of cases suggests higher risk of protozoan infection may exist for some communities. Conclusions These findings provide useful information for policy makers to design and tailor interventions to target high risk communities. Follow-up investigation into the risk factors for giardiasis in regional/rural areas is needed.

Flood, PJ, Yin, L, Herdean, A, Harbinson, J, Aarts, MGM & Spetea, C 2014, 'Natural variation in phosphorylation of photosystem II proteins in Arabidopsis thaliana : is it caused by genetic variation in the STN kinases?', Philosophical Transactions of the Royal Society B: Biological Sciences, vol. 369, no. 1640, pp. 20130499-20130499.
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Reversible phosphorylation of photosystem II (PSII) proteins is an important regulatory mechanism that can protect plants from changes in ambient light intensity and quality. We hypothesized that there is natural variation in this process in Arabidopsis ( Arabidopsis thaliana ), and that this results from genetic variation in the STN7 and STN8 kinase genes. To test this, Arabidopsis accessions of diverse geographical origins were exposed to two light regimes, and the levels of phospho-D1 and phospho-light harvesting complex II (LHCII) proteins were quantified by western blotting with anti-phosphothreonine antibodies. Accessions were classified as having high, moderate or low phosphorylation relative to Col-0. This variation could not be explained by the abundance of the substrates in thylakoid membranes. In genotypes with atrazine-resistant forms of the D1 protein, low D1 and LHCII protein phosphorylation was observed, which may be due to low PSII efficiency, resulting in reduced activation of the STN kinases. In the remaining genotypes, phospho-D1 levels correlated with STN8 protein abundance in high-light conditions. In growth light, D1 and LHCII phosphorylation correlated with longitude and in the case of LHCII phosphorylation also with temperature variability. This suggests a possible role of natural variation in PSII protein phosphorylation in the adaptation of Arabidopsis to diverse environments.

Flores-Molina, MR, Thomas, D, Lovazzano, C, Núñez, A, Zapata, J, Kumar, M, Correa, JA & Contreras-Porcia, L 2014, 'Desiccation stress in intertidal seaweeds: Effects on morphology, antioxidant responses and photosynthetic performance', Aquatic Botany, vol. 113, pp. 90-99.
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Seaweeds are differentially distributed between the upper and lower limits of the intertidal zone of rocky coasts around the world. Daily changes in tide height cause water loss, triggering desiccation stress as a consequence. How this stress affected some of the morphological characteristics and physiological responses in representative intertidal seaweeds with contrasting vertical distributions was explored in the present work. The selected species were Mazzaella laminarioides (upper-middle distribution), Scytosiphon lomentaria and Ulva compressa (middle distribution), and Lessonia spicata and Gelidium rex (lower distribution). To assess tolerance response to desiccation, cellular and morphological alterations, ROS production, enzymatic activity of catalase (CAT) and ascorbate peroxidase (AP) and photosynthesis performance were measured after a simulated emersion stress experiment. Results show different tolerance responses to desiccation, with seaweeds having higher intertidal distributions displaying greater antioxidant enzymatic activity, suggesting a higher capacity to buffer ROS excess induced during desiccation. Contrarily, this capacity seems to be absent or deficient in low intertidal species (i.e. L. spicata and G. rex), where AP and CAT activities were below detection limits, ROS were higher than normal and caused an over-oxidation of bio-molecules and photosynthetic disarray, explaining from a functional stand point their low distribution in the intertidal zone. © 2013 Elsevier B.V.

Fourment, M & Holmes, EC 2014, 'Novel non-parametric models to estimate evolutionary rates and divergence times from heterochronous sequence data', BMC Evolutionary Biology, vol. 14, no. 1, pp. 1-12.
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BACKGROUND: Early methods for estimating divergence times from gene sequence data relied on the assumption of a molecular clock. More sophisticated methods were created to model rate variation and used auto-correlation of rates, local clocks, or the so called "uncorrelated relaxed clock" where substitution rates are assumed to be drawn from a parametric distribution. In the case of Bayesian inference methods the impact of the prior on branching times is not clearly understood, and if the amount of data is limited the posterior could be strongly influenced by the prior. RESULTS: We develop a maximum likelihood method--Physher--that uses local or discrete clocks to estimate evolutionary rates and divergence times from heterochronous sequence data. Using two empirical data sets we show that our discrete clock estimates are similar to those obtained by other methods, and that Physher outperformed some methods in the estimation of the root age of an influenza virus data set. A simulation analysis suggests that Physher can outperform a Bayesian method when the real topology contains two long branches below the root node, even when evolution is strongly clock-like. CONCLUSIONS: These results suggest it is advisable to use a variety of methods to estimate evolutionary rates and divergence times from heterochronous sequence data. Physher and the associated data sets used here are available online at http://code.google.com/p/physher/.

Fowler, AM, Macreadie, PI, Jones, DOB & Booth, DJ 2014, 'A multi-criteria decision approach to decommissioning of offshore oil and gas infrastructure', OCEAN & COASTAL MANAGEMENT, vol. 87, pp. 20-29.
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Thousands of the world's offshore oil and gas structures are approaching obsolescence and will require decommissioning within the next decade. Many nations have blanket regulations requiring obsolete structures to be removed, yet this option is unlikely to yield optimal environmental, societal and economic outcomes in all situations. We propose that nations adopt a flexible approach that allows decommissioning options to be selected from the full range of alternatives (including 'rigs-to-reefs' options) on a case-by-case basis. We outline a method of multi-criteria decision analysis (Multi-criteria Approval, MA) for evaluating and comparing alternative decommissioning options across key selection criteria, including environmental, financial, socioeconomic, and health and safety considerations. The MA approach structures the decision problem, forces explicit consideration of trade-offs and directly involves stakeholder groups in the decision process. We identify major decommissioning options and provide a generic list of selection criteria for inclusion in the MA decision process. To deal with knowledge gaps concerning environmental impacts of decommissioning, we suggest that expert opinion feed into the MA approach until sufficient data become available. We conducted a limited trial of the MA decision approach to demonstrate its application to a complex and controversial decommissioning scenario; Platform Grace in southern California. The approach indicated, for this example, that the option 'leave in place intact' would likely provide best environmental outcomes in the event of future decommissioning. In summary, the MA approach will allow the environmental, social, and economic impacts of decommissioning decisions to be assessed simultaneously in a transparent manner. © 2013 Elsevier Ltd.

Fox, GJ, Sy, DN, Nhung, NV, Yu, B, Ellis, MK, Van Hung, N, Cuong, NK, Thi Lien, L, Marks, GB, Saunders, BM & Britton, WJ 2014, 'Polymorphisms of SP110 Are Associated with both Pulmonary and Extra-Pulmonary Tuberculosis among the Vietnamese', PLoS ONE, vol. 9, no. 7, pp. e99496-e99496.
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Tuberculosis (TB) is an infectious disease that remains a major cause of morbidity and mortality worldwide, yet the reasons why only 10% of people infected with Mycobacterium tuberculosis go on to develop clinical disease are poorly understood. Genetically determined variation in the host immune response is one factor influencing the response to M. tuberculosis. SP110 is an interferon-responsive nuclear body protein with critical roles in cell cycling, apoptosis and immunity to infection. However association studies of the gene with clinical TB in different populations have produced conflicting results.To examine the importance of the SP110 gene in immunity to TB in the Vietnamese we conducted a case-control genetic association study of 24 SP110 variants, in 663 patients with microbiologically proven TB and 566 unaffected control subjects from three tertiary hospitals in northern Vietnam.Five SNPs within SP110 were associated with all forms of TB, including four SNPs at the C terminus (rs10208770, rs10498244, rs16826860, rs11678451) under a dominant model and one SNP under a recessive model, rs7601176. Two of these SNPs were associated with pulmonary TB (rs10208770 and rs16826860) and one with extra-pulmonary TB (rs10498244).SP110 variants were associated with increased susceptibility to both pulmonary and extra-pulmonary TB in the Vietnamese. Genetic variants in SP110 may influence macrophage signaling responses and apoptosis during M. tuberculosis infection, however further research is required to establish the mechanism by which SP110 influences immunity to tuberculosis infection.

Franklin, BS, Bossaller, L, De Nardo, D, Ratter, JM, Stutz, A, Engels, G, Brenker, C, Nordhoff, M, Mirandola, SR, Al-Amoudi, A, Mangan, MS, Zimmer, S, Monks, BG, Fricke, M, Schmidt, RE, Espevik, T, Jones, B, Jarnicki, AG, Hansbro, PM, Busto, P, Marshak-Rothstein, A, Hornemann, S, Aguzzi, A, Kastenmüller, W & Latz, E 2014, 'The adaptor ASC has extracellular and 'prionoid' activities that propagate inflammation', Nature Immunology, vol. 15, no. 8, pp. 727-737.
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Microbes or danger signals trigger inflammasome sensors, which induce polymerization of the adaptor ASC and the assembly of ASC specks. ASC specks recruit and activate caspase-1, which induces maturation of the cytokine interleukin 1β (IL-1β) and pyroptotic cell death. Here we found that after pyroptosis, ASC specks accumulated in the extracellular space, where they promoted further maturation of IL-1β. In addition, phagocytosis of ASC specks by macrophages induced lysosomal damage and nucleation of soluble ASC, as well as activation of IL-1β in recipient cells. ASC specks appeared in bodily fluids from inflamed tissues, and autoantibodies to ASC specks developed in patients and mice with autoimmune pathologies. Together these findings reveal extracellular functions of ASC specks and a previously unknown form of cell-to-cell communication. © 2014 Nature America, Inc. All rights reserved.

Fricker, M, Deane, A & Hansbro, PM 2014, 'Animal models of chronic obstructive pulmonary disease', Expert Opinion on Drug Discovery, vol. 9, no. 6, pp. 629-645.
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Introduction

Chronic obstructive pulmonary disease (COPD) is a leading global cause of mortality and chronic morbidity. Inhalation of cigarette smoke is the principal risk factor for development of this disease. COPD is a progressive disease that is typically characterised by chronic pulmonary inflammation, mucus hypersecretion, airway remodelling and emphysema that collectively reduce lung function. There are currently no therapies that effectively halt or reverse disease progression. It is hoped that the development of animal models that develop the hallmark features of COPD, in a short time frame, will aid in the identifying and testing of new therapeutic approaches.

Areas covered

The authors review the recent developments in mouse models of chronic cigarette smoke-induced COPD as well as the principal findings. Furthermore, the authors discuss the use of mouse models to understand the pathogenesis and the contribution of infectious exacerbations. They also discuss the investigations of the systemic co-morbidities of COPD (pulmonary hypertension, cachexia and osteoporosis).

Expert opinion

Recent advances in the field mark a point where animal models recapitulate the pathologies of COPD patients in a short time frame. They also reveal novel insights into the pathogenesis and potential treatment of this debilitating disease.

Fricker, M, Walker, MM, Talley, NJ, Keely, S & Hansbro, P 2014, 'Tu1732 Colon Pathology in a Mouse Model of Cigarette Smoke Induced Chronic Obstructive Pulmonary Disease (COPD) -A Model for Induction of Crohn's Disease?', Gastroenterology, vol. 146, no. 5.
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Fu, F, Wu, Y, Zhu, J, Wen, S, Shen, M & Shi, X 2014, 'Multifunctional Lactobionic Acid-Modified Dendrimers for Targeted Drug Delivery to Liver Cancer Cells: Investigating the Role Played by PEG Spacer', ACS Applied Materials & Interfaces, vol. 6, no. 18, pp. 16416-16425.
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Fu, S, Luong, S, Pham, A, Charlton, N & Kuzhiumparambil, U 2014, 'Bioanalysis of urine samples after manipulation by oxidizing chemicals: technical considerations', BIOANALYSIS, vol. 6, no. 11, pp. 1543-1561.
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Fung, T, Wang, JJJ & Seneta, E 2014, 'The Deviance Information Criterion in Comparison of Normal Mixing Models', International Statistical Review, vol. 82, no. 3, pp. 411-421.
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SummaryModel selection from several non‐nested models by using the deviance information criterion within Bayesian inference Using Gibbs Sampling (BUGS) software needs to be treated with caution. This is particularly important if one can specify a model in various mixing representations, as for the normal variance‐mean mixing distribution occurring in financial contexts. We propose a procedure to compare goodness of fit of several non‐nested models, which uses BUGS software in part.

Gadau, M, Yeung, W-F, Liu, H, Zaslawski, C, Tan, Y-S, Wang, F-C, Bangrazi, S, Chung, K-F, Bian, Z-X, Zhang, S-P & Study, TEAI 2014, 'Acupuncture and moxibustion for lateral elbow pain: a systematic review of randomized controlled trials', BMC COMPLEMENTARY AND ALTERNATIVE MEDICINE, vol. 14.
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Background: Acupuncture and moxibustion have widely been used to treat lateral elbow pain (LEP). A comprehensive systematic review of randomized controlled trials (RCTs) including both English and Chinese databases was conducted to assess the efficacy of acupuncture and moxibustion in the treatment of LEP.Methods: Revised STRICTA (2010) criteria were used to appraise the acupuncture procedures, the Cochrane risk of bias tool was used to assess the methodological quality of the studies. A total of 19 RCTs that compared acupuncture and/or moxibustion with sham acupuncture, another form of acupuncture, or conventional treatment were included.Results: All studies had at least one domain rated as high risk or uncertain risk of bias in the Cochrane risk of bias tool. Results from three RCTs of moderate quality showed that acupuncture was more effective than sham acupuncture. Results from 10 RCTs of mostly low quality showed that acupuncture or moxibustion was superior or equal to conventional treatment, such as local anesthetic injection, local steroid injection, non-steroidal anti- inflammatory drugs, or ultrasound. There were six low quality RCTs that compared acupuncture and moxibustion combined with manual acupuncture alone, and all showed that acupuncture and moxibustion combined was superior to manual acupuncture alone.Conclusion: Moderate quality studies suggest that acupuncture is more effective than sham acupuncture. Interpretations of findings regarding acupuncture vs. conventional treatment, and acupuncture and moxibustion combined vs. manual acupuncture alone are limited by the methodological qualities of these studies. Future studies with improved methodological design are warranted to confirm the efficacy of acupuncture and moxibustion for LEP. © 2014 Gadau et al.; licensee BioMed Central Ltd.

Gann, E, McNeill, CR, Szumilo, M, Sirringhaus, H, Sommer, M, Maniam, S, Langford, SJ & Thomsen, L 2014, 'Near-edge X-ray absorption fine-structure spectroscopy of naphthalene diimide-thiophene co-polymers', The Journal of Chemical Physics, vol. 140, no. 16, pp. 164710-164710.
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Near-edge X-ray absorption fine-structure (NEXAFS) spectroscopy is an important tool for probing the structure of conjugated polymer films used in organic electronic devices. High-performance conjugated polymers are often donor-acceptor co-polymers which feature a repeat unit with multiple functional groups. To facilitate better application of NEXAFS spectroscopy to the study of such materials, improved understanding of the observed NEXAFS spectral features is required. In order to examine how the NEXAFS spectrum of a donor-acceptor co-polymer relates to the properties of the sub-units, a series of naphthalene diimide-thiophene-based co-polymers have been studied where the nature and length of the donor co-monomer has been systematically varied. The spectra of these materials are compared with that of a thiophene homopolymer and naphthalene diimide monomer enabling peak assignment and the influence of inter-unit electronic coupling to be assessed. We find that while it is possible to attribute peaks within the π* manifold as arising primarily due to the naphthalene diimide or thiophene sub-units, very similar dichroism of these peaks is observed indicating that it may not be possible to separately probe the molecular orientation of the separate sub-units with carbon K-edge NEXAFS spectroscopy.

Garcia, TP, Müller, S, Carroll, RJ & Walzem, RL 2014, 'Identification of important regressor groups, subgroups and individuals via regularization methods: application to gut microbiome data', Bioinformatics, vol. 30, no. 6, pp. 831-837.
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AbstractMotivation: Gut microbiota can be classified at multiple taxonomy levels. Strategies to use changes in microbiota composition to effect health improvements require knowing at which taxonomy level interventions should be aimed. Identifying these important levels is difficult, however, because most statistical methods only consider when the microbiota are classified at one taxonomy level, not multiple.Results: Using L1 and L2 regularizations, we developed a new variable selection method that identifies important features at multiple taxonomy levels. The regularization parameters are chosen by a new, data-adaptive, repeated cross-validation approach, which performed well. In simulation studies, our method outperformed competing methods: it more often selected significant variables, and had small false discovery rates and acceptable false-positive rates. Applying our method to gut microbiota data, we found which taxonomic levels were most altered by specific interventions or physiological status.Availability: The new approach is implemented in an R package, which is freely available from the corresponding author.Contact: tpgarcia@srph.tamhsc.eduSupplementary information:  Supplementary data are available at Bioinformatics online.

Garren, M, Son, K, Raina, J-B, Rusconi, R, Menolascina, F, Shapiro, OH, Tout, J, Bourne, DG, Seymour, JR & Stocker, R 2014, 'A bacterial pathogen uses dimethylsulfoniopropionate as a cue to target heat-stressed corals', ISME JOURNAL, vol. 8, no. 5, pp. 999-1007.
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Diseases are an emerging threat to ocean ecosystems. Coral reefs, in particular, are experiencing a worldwide decline because of disease and bleaching, which have been exacerbated by rising seawater temperatures. Yet, the ecological mechanisms behind most coral diseases remain unidentified. Here, we demonstrate that a coral pathogen, Vibrio coralliilyticus, uses chemotaxis and chemokinesis to target the mucus of its coral host, Pocillopora damicornis. A primary driver of this response is the host metabolite dimethylsulfoniopropionate (DMSP), a key element in the global sulfur cycle and a potent foraging cue throughout the marine food web. Coral mucus is rich in DMSP, and we found that DMSP alone elicits chemotactic responses of comparable intensity to whole mucus. Furthermore, in heat-stressed coral fragments, DMSP concentrations increased fivefold and the pathogen's chemotactic response was correspondingly enhanced. Intriguingly, despite being a rich source of carbon and sulfur, DMSP is not metabolized by the pathogen, suggesting that it is used purely as an infochemical for host location. These results reveal a new role for DMSP in coral disease, demonstrate the importance of chemical signaling and swimming behavior in the recruitment of pathogens to corals and highlight the impact of increased seawater temperatures on disease pathways. © 2014 International Society for Microbial Ecology All rights reserved.

Gentle, AR & Smith, GB 2014, 'Procedure for measuring simultaneously the solar and visible properties of glazing with complex internal or external structures', APPLIED OPTICS, vol. 53, no. 30, pp. 7157-7167.
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Giannitti, F, Barr, BC, Brito, BP, Uzal, FA, Villanueva, M & Anderson, M 2014, 'Yersinia pseudotuberculosis infections in goats and other animals diagnosed at the California Animal Health and Food Safety Laboratory System: 1990–2012', Journal of Veterinary Diagnostic Investigation, vol. 26, no. 1, pp. 88-95.
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Yersinia pseudotuberculosis is a recognized zoonotic food-borne pathogen; however, little is known about the ecology and epidemiology of diseases caused by the bacterium in California. The objective of the current study was to contribute to the knowledge of the diseases caused by Y. pseudotuberculosis in goats, the animal species most frequently reported with clinical yersiniosis to the California Animal Health and Food Safety Laboratory System, to better understand the epidemiology of this disease. A 23-year retrospective study was conducted to characterize the syndromes caused by the bacterium in goats and their temporospatial distribution, and to determine the number of cases in other animal species. Yersinia pseudotuberculosis–associated disease was diagnosed in 42 goats from 21 counties, with a strong seasonality in winter and spring. Most cases (88%) were observed within particular years (1999, 2004–2006, 2010–2011). The most frequently diagnosed syndrome was enteritis and/or typhlocolitis (64.3%), followed by abscessation (14.3%), abortion (11.9%), conjunctivitis (4.75%), and hepatitis (4.75%). Among other animal species, 59 cases were diagnosed in non-poultry avian species and 33 in mammals other than goats.

Giunta, S, Andriolo, V & Castorina, A 2014, 'Dual blockade of the A1 and A2A adenosine receptor prevents amyloid beta toxicity in neuroblastoma cells exposed to aluminum chloride', The International Journal of Biochemistry & Cell Biology, vol. 54, pp. 122-136.
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Gladstone, W 2014, 'Criticisms of science, social impacts, opinion leaders, and targets for no‐take zones led to cuts in New South Wales' (Australia) system of marine protected areas', Aquatic Conservation: Marine and Freshwater Ecosystems, vol. 24, no. 3, pp. 287-296.
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On 12 March 2013 the state Government of New South Wales (NSW), Australia, announced a new approach to managing its marine environment (including calling it the `marine estate). This included announcing an amnesty on recreational shore-based fishing in all ocean beach and headland sanctuary zones (i.e. no-take) in its State-wide system of large multiple-use marine protected areas (MPAs), called marine parks, and a moratorium on declaring more marine parks (NSW Government, 2013a). The NSW Government Ministers responsible for marine parks stated `decisions around the management of the NSW marine estate will now be based on science and in the long term interest of community, marine ecosystems and industry. The NSW Government is delivering on its election commitment for a common sense marine parks policyAfter years of political interference and decisions based on poor or incomplete sciencethe credibility of Marine Parks and our fishing industries has been undermined (NSW Government, 2013a), and `There is little or no scientific basis for preventing line fishing from landWe are immediately giving an amnesty to that (The Coffs Coast Advocate, 2013). Despite the relatively minor change in total area of no-take zones in NSWs marine parks this decision attracted the most attention from conservation groups, recreational fishing groups and scientists. However, the changes announced also included a potentially far-reaching shift in policy approach to biodiversity conservation away from the nationally agreed precautionary use of a representative network of MPAs to a risk-based framework. Australia has been implementing a National Representative System of Marine Protected Areas (NRSMPA) as a uniform national approach to conserve marine biodiversity. In 1998 the governments of Australia with marine coasts (i.e. the Commonwealth, all States, the Northern Territory) undertook to establish the NRSMPA by 2012 to achieve national goals for sustainable development (Commonwealth of Au...

Gladstone, W & Courtenay, G 2014, 'Impacts of docks on seagrass and effects of management practices to ameliorate these impacts', ESTUARINE COASTAL AND SHELF SCIENCE, vol. 136, pp. 53-60.
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Seagrasses have high conservation and human-use values, but around the world they are being damaged by human activities. Compared to the larger spatial scale at which some human activities affect estuaries and their seagrasses (e.g. catchment disturbance, dredging, pollution, trawling), recreational boating and infrastructure of moorings and docks act at smaller scales. However, the cumulative effects contribute to stresses acting on seagrass beds. This study assessed the effects of docks on the native seagrass Zostera muelleri subsp. capricorni in an estuary in south-east Australia and of current management practices designed to reduce dock impacts on this seagrass. A field survey found that seagrass biomass was significantly reduced below docks, and the effects were not influenced by dock orientation. Management practices requiring the use of a mesh decking to provide greater light penetration reduced, but did not eliminate, the reduction in seagrass biomass caused by docks. A modified beyond BACI experiment provided evidence for a causal link between the installation of wooden or mesh docks and reductions in biomass of seagrass. The reduction in biomass was apparent 6 mo after dock installation, and by 26 mo seagrass biomass had declined by at least 90%. Faced with increasing coastal populations, increases in recreational use, and continued pressures from other human activities, alternative management practices that further minimize the effects of docks are needed.

Gleason, SM, Blackman, CJ, Cook, AM, Laws, CA & Westoby, M 2014, 'Whole-plant capacitance, embolism resistance and slow transpiration rates all contribute to longer desiccation times in woody angiosperms from arid and wet habitats', Tree Physiology, vol. 34, no. 3, pp. 275-284.
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Godecke, E, Armstrong, E, Middleton, S, Rai, T, Holland, AE, Cadilhac, D, Whitworth, A, Rose, M, Ciccone, N, Hankey, G & Bernhardt, J 2014, 'Very Early Rehabilitation in SpEech (VERSE): Progress report', INTERNATIONAL JOURNAL OF STROKE, vol. 9, pp. 48-48.

Godecke, E, Ciccone, NA, Granger, AS, Rai, T, West, D, Cream, A, Cartwright, J & Hankey, GJ 2014, 'A comparison of aphasia therapy outcomes before and after a Very Early Rehabilitation programme following stroke', INTERNATIONAL JOURNAL OF LANGUAGE & COMMUNICATION DISORDERS, vol. 49, no. 2, pp. 149-161.
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Background Very early aphasia rehabilitation studies have shown mixed results. Differences in therapy intensity and therapy type contribute significantly to the equivocal results. Aims To compare a standardized, prescribed very early aphasia therapy regimen with a historical usual care control group at therapy completion (4-5 weeks post-stroke) and again at follow-up (6 months). Methods & Procedures This study compared two cohorts from successive studies conducted in four Australian acute/sub-acute hospitals. The studies had near identical recruitment, blinded assessment and data-collection protocols. The Very Early Rehabilitation (VER) cohort (N = 20) had mild-severe aphasia and received up to 20 1-h sessions of impairment-based aphasia therapy, up to 5 weeks. The control cohort (n = 27) also had mild-severe aphasia and received usual care (UC) therapy for up to 4 weeks post-stroke. The primary outcome measure was the Aphasia Quotient (AQ) and a measure of communicative efficiency (DA) at therapy completion. Outcomes were measured at baseline, therapy completion and 6 months post-stroke and were compared using Generalised Estimating Equations (GEE) models. Outcomes & Results After controlling for initial aphasia and stroke disability, the GEE models demonstrated that at the primary end-point participants receiving VER achieved 18% greater recovery on the AQ and 1.5% higher DA scores than those in the control cohort. At 6 months, the VER participants maintained a 16% advantage in recovery on the AQ and 0.6% more on DA scores over the control cohort participants. Conclusions & Implications A prescribed, impairment-based aphasia therapy regimen, provided daily in very early post-stroke recovery, resulted in significantly greater communication gains in people with mild-severe aphasia at completion of therapy and at 6 months, when compared with a historical control cohort. Further research is required to demonstrate large-scale and long-term efficacy. © 201...

Goerigk, L, Collyer, CA & Reimers, JR 2014, 'Recommending Hartree–Fock Theory with London-Dispersion and Basis-Set-Superposition Corrections for the Optimization or Quantum Refinement of Protein Structures', The Journal of Physical Chemistry B, vol. 118, no. 50, pp. 14612-14626.
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© 2014 American Chemical Society. We demonstrate the importance of properly accounting for London dispersion and basis-set-superposition error (BSSE) in quantum-chemical optimizations of protein structures, factors that are often still neglected in contemporary applications. We optimize a portion of an ensemble of conformationally flexible lysozyme structures obtained from highly accurate X-ray crystallography data that serve as a reliable benchmark. We not only analyze root-mean-square deviations from the experimental Cartesian coordinates, but also, for the first time, demonstrate how London dispersion and BSSE influence crystallographic R factors. Our conclusions parallel recent recommendations for the optimization of small gas-phase peptide structures made by some of the present authors: Hartree-Fock theory extended with Grimme's recent dispersion and BSSE corrections (HF-D3-gCP) is superior to popular density functional theory (DFT) approaches. Not only are statistical errors on average lower with HF-D3-gCP, but also the convergence behavior is much better. In particular, we show that the BP86/6-31G∗ approach should not be relied upon as a black-box method, despite its widespread use, as its success is based on an unpredictable cancellation of errors. Using HF-D3-gCP is technically straightforward, and we therefore encourage users of quantum-chemical methods to adopt this approach in future applications. (Chemical Presented).

Gonçalves, LFFF, Kanodarwala, FK, Stride, JA, Silva, CJR, Pereira, MR & Gomes, MJM 2014, 'One-pot synthesis of CdSe nanoparticles exhibiting quantum size effect within a sol–gel derived ureasilicate matrix', Journal of Photochemistry and Photobiology A: Chemistry, vol. 285, pp. 21-29.
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Gonçalves, LFFF, Silva, CJR, Kanodarwala, FK, Stride, JA & Gomes, MJM 2014, 'Synthesis and characterization of organic–inorganic hybrid materials prepared by sol–gel and containing CdS nanoparticles prepared by a colloidal method using poly(N-vinyl-2-pyrrolidone)', Journal of Sol-Gel Science and Technology, vol. 71, no. 1, pp. 69-78.
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Gonçalves, LFFF, Silva, CJR, Kanodarwala, FK, Stride, JA, Pereira, MR & Gomes, MJM 2014, 'Influence of Cd 2+ /S 2− molar ratio and of different capping environments in the optical properties of CdS nanoparticles incorporated within a hybrid diureasil matrix', Applied Surface Science, vol. 314, pp. 877-887.
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Gonçalves, LFFF, Silva, CJR, Kanodarwala, FK, Stride, JA, Pereira, MR & Gomes, MJM 2014, 'Synthesis of an optically clear, flexible and stable hybrid ureasilicate matrix doped with CdSe nanoparticles produced by reverse micelles', Materials Chemistry and Physics, vol. 147, no. 1-2, pp. 86-94.
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Goodswen, SJ, Kennedy, PJ & Ellis, JT 2014, 'Discovering a vaccine against neosporosis using computers: is it feasible?', TRENDS IN PARASITOLOGY, vol. 30, no. 8, pp. 401-411.
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Goodswen, SJ, Kennedy, PJ & Ellis, JT 2014, 'Enhancing In Silico Protein-Based Vaccine Discovery for Eukaryotic Pathogens Using Predicted Peptide-MHC Binding and Peptide Conservation Scores', PLOS ONE, vol. 9, no. 12.
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Goodswen, SJ, Kennedy, PJ & Ellis, JT 2014, 'Vacceed: a high-throughput in silico vaccine candidate discovery pipeline for eukaryotic pathogens based on reverse vaccinology', BIOINFORMATICS, vol. 30, no. 16, pp. 2381-2383.
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Summary: We present Vacceed, a highly configurable and scalable framework designed to automate the process of high-throughput in silico vaccine candidate discovery for eukaryotic pathogens. Given thousands of protein sequences from the target pathogen as input, the main output is a ranked list of protein candidates determined by a set of machine learning algorithms. Vacceed has the potential to save time and money by reducing the number of false candidates allocated for laboratory validation. Vacceed, if required, can also predict protein sequences from the pathogen's genome. © The Author 2014.

Gorle, AK, Ammit, AJ, Wallace, L, Keene, FR & Collins, JG 2014, 'Multinuclear ruthenium(ii) complexes as anticancer agents', New J. Chem., vol. 38, no. 9, pp. 4049-4059.
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The dinuclear ruthenium complex with X = H is four-times more cytotoxic than cisplatin against breast cancer cell lines; however, when X = NO₂ the ruthenium complex is less active than cisplatin.

Grafton, KT, Moir, LM, Black, JL, Hansbro, NG, Hansbro, PM, Burgess, JK & Oliver, BG 2014, 'LF-15 & T7, Synthetic Peptides Derived from Tumstatin, Attenuate Aspects of Airway Remodelling in a Murine Model of Chronic OVA-Induced Allergic Airway Disease', PLOS ONE, vol. 9, no. 1, pp. 1-6.
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Background: Tumstatin is a segment of the collagen-IV protein that is markedly reduced in the airways of asthmatics. Tumstatin can play an important role in the development of airway remodelling associated with asthma due to its antiangiogenic properties. This study assessed the anti-angiogenic properties of smaller peptides derived from tumstatin, which contain the interface tumstatin uses to interact with the aVb3 integrin. Methods: Primary human lung endothelial cells were exposed to the LF-15, T3 and T7 tumstatin-derived peptides and assessed for cell viability and tube formation in vitro. The impact of the anti-angiogenic properties on airways hyperresponsiveness (AHR) was then examined using a murine model of chronic OVA-induced allergic airways disease. Results: The LF-15 and T7 peptides significantly reduced endothelial cell viability and attenuated tube formation in vitro. Mice exposed to OVA+ LF-15 or OVA+T7 also had reduced total lung vascularity and AHR was attenuated compared to mice exposed to OVA alone. T3 peptides reduced cell viability but had no effect on any other parameters. Conclusion: The LF-15 and T7 peptides may be appropriate candidates for use as novel pharmacotherapies due to their small size and anti-angiogenic properties observed in vitro and in vivo. © 2014 Grafton et al.

Greaves, IK, Groszmann, M, Wang, A, Peacock, WJ & Dennis, ES 2014, 'Inheritance of Trans Chromosomal Methylation patterns from Arabidopsis F1 hybrids', PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 111, no. 5, pp. 2017-2022.
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Groszmann, M, Gonzalez-Bayon, R, Greaves, IK, Wang, L, Huen, AK, Peacock, WJ & Dennis, ES 2014, 'Intraspecific Arabidopsis Hybrids Show Different Patterns of Heterosis Despite the Close Relatedness of the Parental Genomes', PLANT PHYSIOLOGY, vol. 166, no. 1, pp. 265-+.
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Growns, I, Chessman, B, Mitrovic, S & Westhorpe, D 2014, 'The effects of dams on longitudinal variation in river food webs', JOURNAL OF FRESHWATER ECOLOGY, vol. 29, no. 1, pp. 69-82.
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We examined the effects of two dams on longitudinal variation of riverine food webs using stable isotope and gut contents analyses along four rivers in the Hunter Valley in eastern Australia. Longitudinal 15N enrichment was observed in most invertebrate taxa and food sources but significant longitudinal variation was rare for 13C, and composition of gut contents of invertebrate taxa did not vary significantly with longitudinal position. Most invertebrates and food sources were more 15N-enriched at sites immediately downstream of the dams than expected from their upstream longitudinal position, a result not mirrored by gut contents and 13C. Enrichment of 15N downstream may be attributed to altered water quality as a result of impoundment but further research is necessary to elucidate whether physico-chemical riverine processes or trophic mechanisms are responsible. Our observations regarding the influence of dams on isotope ratios are contrary to the few existing studies, suggesting the small volumes relative to annual inflows of dams in the present study limit downstream impacts by maintaining aspects of flow variability.

Guan, J, Zhang, Y, Zhou, G, Wang, C, Qu, Q, Hu, X & Wang, G 2014, 'DETERMINATION OF PROLINE, HYDROXYPROLINE, AND N–ETHYLGLYCINE IN URINE BY USING A NEW HPLC LABELING REAGENT, AND ITS APPLICATION IN DETECTION OF TUMOR MARKERS', Journal of Liquid Chromatography & Related Technologies, vol. 37, no. 12, pp. 1731-1749.
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According to previous reports, the concentration of urinary proline (Pro), hydroxyproline (Hyp), and N-ethylglycine (Neg) varies in association with various diseases, especially, Neg as a tumor marker was recently found in association with bone metastasis cancers. We developed a low-cost, highly sensitive precolumn high-performance liquid chromatography (HPLC) method for simultaneous determination of Pro, Hyp, and Neg in urine of patients with cancers, bone metastasis cancers, and bone metastasis cancers that have appeared after radiotherapy and chemotherapy treatment. The analytes in the urine were labeled with 4-methoxybenzenesulfonyl fluoride (MOBS-F) at 40°C. The derivatives were separated on a reversed-phase column by gradient elution and monitored with ultraviolet (UV) detection at 232 nm. The detection limits for Pro, Hyp, and Neg were 6.0 pmol/injection, 4.0 pmol/injection, and 50 pmol/injection (S/N = 3), respectively. To some extent, Neg levels in their urine show there were relevance to their health conditions or therapy progress. We believe that the developed method may be a promising measure for providing a useful reference to diagnose the illness and monitor the results for bone metastasis cancers after radiotherapy and chemotherapy treatment. © 2014 Copyright Taylor & Francis Group, LLC.

Guanter, L, Zhang, Y, Jung, M, Joiner, J, Voigt, M, Berry, JA, Frankenberg, C, Huete, AR, Zarco-Tejada, P, Lee, J-E, Moran, MS, Ponce-Campos, G, Beer, C, Camps-Valls, G, Buchmann, N, Gianelle, D, Klumpp, K, Cescatti, A, Baker, JM & Griffis, TJ 2014, 'Global and time-resolved monitoring of crop photosynthesis with chlorophyll fluorescence', PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 111, no. 14, pp. E1327-E1333.
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Photosynthesis is the process by which plants harvest sunlight to produce sugars from carbon dioxide and water. It is the primary source of energy for all life on Earth; hence it is important to understand how this process responds to climate change and human impact. However, model-based estimates of gross primary production (GPP, output from photosynthesis) are highly uncertain, in particular over heavily managed agricultural areas. Recent advances in spectroscopy enable the space-based monitoring of sun-induced chlorophyll fluorescence (SIF) from terrestrial plants. Here we demonstrate that spaceborne SIF retrievals provide a direct measure of the GPP of cropland and grassland ecosystems. Such a strong link with crop photosynthesis is not evident for traditional remotely sensed vegetation indices, nor for more complex carbon cycle models. We use SIF observations to provide a global perspective on agricultural productivity. Our SIF-based crop GPP estimates are 50-75% higher than results from state-ofthe- art carbon cycle models over, for example, the US Corn Belt and the Indo-Gangetic Plain, implying that current models severely underestimate the role of management. Our results indicate that SIF data can help us improve our global models for more accurate projections of agricultural productivity and climate impact on crop yields. Extension of our approach to other ecosystems, along with increased observational capabilities for SIF in the near future, holds the prospect of reducing uncertainties in the modeling of the current and future carbon cycle.

Guenther, PM, Kirkpatrick, SI, Reedy, J, Krebs-Smith, SM, Buckman, DW, Dodd, KW, Casavale, KO & Carroll, RJ 2014, 'The Healthy Eating Index-2010 Is a Valid and Reliable Measure of Diet Quality According to the 2010 Dietary Guidelines for Americans', The Journal of Nutrition, vol. 144, no. 3, pp. 399-407.
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The Healthy Eating Index (HEI), a measure of diet quality, was updated to reflect the 2010 Dietary Guidelines for Americans and the accompanying USDA Food Patterns. To assess the validity and reliability of the HEI-2010, exemplary menus were scored and 2 24-h dietary recalls from individuals aged ≥2 y from the 2003-2004 NHANES were used to estimate multivariate usual intake distributions and assess whether the HEI-2010 1) has a distribution wide enough to detect meaningful differences in diet quality among individuals, 2) distinguishes between groups with known differences in diet quality by using t tests, 3) measures diet quality independently of energy intake by using Pearson correlation coefficients, 4) has > 1 underlying dimension by using principal components analysis (PCA), and 5) is internally consistent by calculating Cronbach's coefficient α. HEI-2010 scores were at or near the maximum levels for the exemplary menus. The distribution of scores among the population was wide (5th percentile = 31.7; 95th percentile = 70.4). As predicted, men's diet quality (mean HEI-2010 total score = 49.8) was poorer than women's (52.7), younger adults' diet quality (45.4) was poorer than older adults' (56.1), and smokers' diet quality (45.7) was poorer than nonsmokers' (53.3) (P < 0.01). Low correlations with energy were observed for HEI-2010 total and component scores (|r| ≤ 0.21). Cronbach's coefficient a was 0.68, supporting the reliability of the HEI-2010 total score as an indicator of overall diet quality. Nonetheless, PCA indicated multiple underlying dimensions, highlighting the fact that the component scores are equally as important as the total. A comparable reevaluation of the HEI-2005 yielded similar results. This study supports the validity and the reliability of both versions of the HEI. © 2014 American Society for Nutrition.

Gunawan, C, Lim, M, Marquis, CP & Amal, R 2014, 'Nanoparticle–protein corona complexes govern the biological fates and functions of nanoparticles', Journal of Materials Chemistry B, vol. 2, no. 15, pp. 2060-2060.
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Upon contact with plasma or other protein-containing biological fluids, the surface of nanoparticles is immediately decorated with proteins forming a biologically active protein corona. The biological fates and functions of nanoparticles are determined by physiological responses toward these nanoparticle-protein corona complexes as the effective biological unit of nanoparticles. In this article, we review representative studies on the effects of particle physicochemical characteristics along with the protein profiles in the biological medium on the formation of protein corona and importantly, how the dynamic nature and protein fingerprints of the formed corona govern the biological responses toward nanoparticles. The biological effects arising from the presence of protein corona can be both beneficial and unfavourable to the biomedical applications of nanoparticles. The protein corona-cell interactions open up the feasibility of targeted delivery and cell-specific uptake of therapeutic nanoparticles and in other circumstances, engineering of nanoparticles as adjuvants for vaccine development as well as mitigation of the unintentional cytotoxic effects of nanoparticles. On the other hand, the protein corona-cell interactions could induce rapid clearance of nanoparticles from in vivo circulation as well as activating unwanted inflammatory responses. Taken together, the knowledge on the formation and biological effects of protein corona enables tailored tuning of the physicochemical characteristics of nanoparticles, unique to their intended biological activity. © 2014 the Partner Organisations.

Gunduz, O, Sahin, YM, Agathopoulos, S, Ben-Nissan, B & Oktar, FN 2014, 'A New Method for Fabrication of Nanohydroxyapatite and TCP from the Sea Snail Cerithium vulgatum', Journal of Nanomaterials, vol. 2014, no. 1, pp. 1-6.
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Biphasic bioceramic nanopowders of hydroxyapatite (HA) and β‐tricalcium phosphate (TCP) were prepared from shells of the sea snail Cerithium vulgatum (Bruguière, 1792) using a novel chemical method. Calcination of the powders produced was carried out at varying temperatures, specifically at 400°C and 800°C, in air for 4 hours. When compared to the conventional hydrothermal transformation method, this chemical method is very simple, economic, due to the fact that it needs inexpensive and safe equipment, because the transformation of the aragonite and calcite of the shells into the calcium phosphate phases takes place at 80°C under the atmospheric pressure. The powders produced were determined using infrared spectroscopy (FT‐IR), X‐ray diffraction, and scanning electron microscopy (SEM). The features of the powders produced along with the fact of their biological origin qualify these powders for further consideration and experimentation to fabricate nanoceramic biomaterials.

Gunn, P, Walsh, S & Roux, C 2014, 'The nucleic acid revolution continues – will forensic biology become forensic molecular biology?', Frontiers in Genetics, vol. 5, no. MAR, pp. 1-4.
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Molecular biology has evolved far beyond that which could have been predicted at the time DNA identity testing was established. Indeed we should now perhaps be referring to 'forensic molecular biology.' Aside from DNA's established role in identifying the 'who' in crime investigations, other developments in medical and developmental molecular biology are now ripe for application to forensic challenges. The impact of DNA methylation and other post-fertilization DNA modifications, plus the emerging role of small RNAs in the control of gene expression, is re-writing our understanding of human biology. It is apparent that these emerging technologies will expand forensic molecular biology to allow for inferences about 'when' a crime took place and 'what' took place. However, just as the introduction of DNA identity testing engendered many challenges, so the expansion of molecular biology into these domains will raise again the issues of scientific validity, interpretation, probative value, and infringement of personal liberties. This Commentary ponders some of these emerging issues, and presents some ideas on how they will affect the conduct of forensic molecular biology in the foreseeable future. © 2014 Gunn, Walsh and Roux.

Guo, H, Chen, Y, Cortie, MB, Liu, X, Xie, Q, Wang, X & Peng, D-L 2014, 'Shape-Selective Formation of Monodisperse Copper Nanospheres and Nanocubes via Disproportionation Reaction Route and Their Optical Properties', JOURNAL OF PHYSICAL CHEMISTRY C, vol. 118, no. 18, pp. 9801-9808.
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Synthesis of stable and monodisperse Cu nanocrystals of controlled morphology has been a long-standing challenge. In this Article, we report a facile disproportionation reaction approach for the synthesis of such nanocrystals in organic solvents. Either spherical or cubic shapes can be produced, depending on conditions. The typical Cu nanospheres are single crystals with a size of 23.4 ± 1.5 nm, and can self-assemble into three-dimensional (3D) nanocrystal superlattices with a large scale. By manipulating the chemical additives, monodisperse Cu nanocubes with tailorable sizes have also been obtained. The probable formation mechanism of these Cu nanocrystals is discussed. The narrow size distribution results in strong surface plasmon resonance (SPR) peaks even though the resonance is located in the interband transition region. Double SPR peaks are observed in the extinction spectra for the Cu nanocubes with relative large sizes. Theoretical simulation of the extinction spectra indicates that the SPR band located at longer wavelengths is caused by assembly of Cu nanocubes into more complex structures. The synthesis procedure that we report here is expected to foster systematic investigations on the physical properties and self-assembly of Cu nanocrystals with shape and size singularity for their potential applications in photonic and nanoelectronic devices. © 2014 American Chemical Society.

Gustafsson, MSM, Baird, ME & Ralph, PJ 2014, 'Modeling photoinhibition-driven bleaching in Scleractinian coral as a function of light, temperature, and heterotrophy', LIMNOLOGY AND OCEANOGRAPHY, vol. 59, no. 2, pp. 603-622.
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Haberle, SG, Bowman, DMJS, Newnham, RM, Johnston, FH, Beggs, PJ, Buters, J, Campbell, B, Erbas, B, Godwin, I, Green, BJ, Huete, A, Jaggard, AK, Medek, D, Murray, F, Newbigin, E, Thibaudon, M, Vicendese, D, Williamson, GJ & Davies, JM 2014, 'The Macroecology of Airborne Pollen in Australian and New Zealand Urban Areas', PLOS ONE, vol. 9, no. 5.
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The composition and relative abundance of airborne pollen in urban areas of Australia and New Zealand are strongly influenced by geographical location, climate and land use. There is mounting evidence that the diversity and quality of airborne pollen is substantially modified by climate change and land-use yet there are insufficient data to project the future nature of these changes. Our study highlights the need for long-term aerobiological monitoring in Australian and New Zealand urban areas in a systematic, standardised, and sustained way, and provides a framework for targeting the most clinically significant taxa in terms of abundance, allergenic effects and public health burden.

Hallstrand, TS, Hackett, TL, Altemeier, WA, Matute-Bello, G, Hansbro, PM & Knight, DA 2014, 'Airway epithelial regulation of pulmonary immune homeostasis and inflammation', Clinical Immunology, vol. 151, no. 1, pp. 1-15.
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Recent genetic, structural and functional studies have identified the airway and lung epithelium as a key orchestrator of the immune response. Further, there is now strong evidence that epithelium dysfunction is involved in the development of inflammatory disorders of the lung. Here we review the characteristic immune responses that are orchestrated by the epithelium in response to diverse triggers such as pollutants, cigarette smoke, bacterial peptides, and viruses. We focus in part on the role of epithelium-derived interleukin (IL)-25, IL-33 and thymic stromal lymphopoietin (TSLP), as well as CC family chemokines as critical regulators of the immune response. We cite examples of the function of the epithelium in host defense and the role of epithelium dysfunction in the development of inflammatory diseases.

Hamidian, M & Hall, RM 2014, 'pACICU2 is a conjugative plasmid of Acinetobacter carrying the aminoglycoside resistance transposon TnaphA6', Journal of Antimicrobial Chemotherapy, vol. 69, no. 4, pp. 1146-1148.
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Hamidian, M & Hall, RM 2014, 'Resistance to third-generation cephalosporins in Acinetobacter baumannii due to horizontal transfer of a chromosomal segment containing ISAba1-ampC', Journal of Antimicrobial Chemotherapy, vol. 69, no. 10, pp. 2865-2866.
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Hamidian, M & Hall, RM 2014, 'Tn6168, a transposon carrying an ISAba1-activated ampC gene and conferring cephalosporin resistance in Acinetobacter baumannii', Journal of Antimicrobial Chemotherapy, vol. 69, no. 1, pp. 77-80.
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Hamidian, M, Holt, KE, Pickard, D, Dougan, G & Hall, RM 2014, 'A GC1 Acinetobacter baumannii isolate carrying AbaR3 and the aminoglycoside resistance transposon TnaphA6 in a conjugative plasmid', Journal of Antimicrobial Chemotherapy, vol. 69, no. 4, pp. 955-958.
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Hamidian, M, Kenyon, JJ, Holt, KE, Pickard, D & Hall, RM 2014, 'A conjugative plasmid carrying the carbapenem resistance gene blaOXA-23 in AbaR4 in an extensively resistant GC1 Acinetobacter baumannii isolate', Journal of Antimicrobial Chemotherapy, vol. 69, no. 10, pp. 2625-2628.
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Hamidian, M, Wynn, M, Holt, KE, Pickard, D, Dougan, G & Hall, RM 2014, 'Identification of a marker for two lineages within the GC1 clone of Acinetobacter baumannii', Journal of Antimicrobial Chemotherapy, vol. 69, no. 2, pp. 557-558.
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Hansbro, PM, Hamilton, MJ, Fricker, M, Gellatly, SL, Jarnicki, AG, Zheng, D, Frei, SM, Wong, GW, Hamadi, S, Zhou, S, Foster, PS, Krilis, SA & Stevens, RL 2014, 'Importance of Mast Cell Prss31/Transmembrane Tryptase/Tryptase-γ in Lung Function and Experimental Chronic Obstructive Pulmonary Disease and Colitis', Journal of Biological Chemistry, vol. 289, no. 26, pp. 18214-18227.
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Protease serine member S31 (Prss31)/transmembrane tryptase/tryptase-γ is a mast cell (MC)-restricted protease of unknown function that is retained on the outer leaflet of the plasma membrane when MCs are activated. We determined the nucleotide sequences of the Prss31 gene in different mouse strains and then used a Cre/loxP homologous recombination approach to create a novel Prss31(-/-) C57BL/6 mouse line. The resulting animals exhibited no obvious developmental abnormality, contained normal numbers of granulated MCs in their tissues, and did not compensate for their loss of the membrane tryptase by increasing their expression of other granule proteases. When Prss31-null MCs were activated with a calcium ionophore or by their high affinity IgE receptors, they degranulated in a pattern similar to that of WT MCs. Prss31-null mice had increased baseline airway reactivity to methacholine but markedly reduced experimental chronic obstructive pulmonary disease and colitis, thereby indicating both beneficial and adverse functional roles for the tryptase. In a cigarette smoke-induced model of chronic obstructive pulmonary disease, WT mice had more pulmonary macrophages, higher histopathology scores, and more fibrosis in their small airways than similarly treated Prss31-null mice. In a dextran sodium sulfate-induced acute colitis model, WT mice lost more weight, had higher histopathology scores, and contained more Cxcl-2 and IL-6 mRNA in their colons than similarly treated Prss31-null mice. The accumulated data raise the possibility that inhibitors of this membrane tryptase may provide additional therapeutic benefit in the treatment of humans with these MC-dependent inflammatory diseases.

Hansbro, PM, Starkey, MR, Mattes, J & Horvat, JC 2014, 'Pulmonary Immunity during Respiratory Infections in Early Life and the Development of Severe Asthma', Annals of the American Thoracic Society, vol. 11, no. Supplement 5, pp. S297-S302.
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Asthma affects 10% of the population in Westernized countries, being most common in children. It is a heterogeneous condition characterized by chronic allergic airway inflammation, mucus hypersecretion, and airway hyperresponsiveness (AHR) to normally innocuous antigens. Combination therapies with inhaled corticosteroids and bronchodilators effectively manage mild to moderate asthma, but there are no cures, and patients with severe asthma do not respond to these treatments. The inception of asthma is linked to respiratory viral (respiratory syncytial virus, rhinovirus) and bacterial (Chlamydia, Mycoplasma) infections. The examination of mouse models of early-life infections and allergic airway disease (AAD) provides valuable insights into the mechanisms of disease inception that may lead to the development of more effective therapeutics. For example, early-life, but not adult, Chlamydia respiratory infections in mice permanently modify immunity and lung physiology. This increases the severity of AAD by promoting IL-13 expression, mucus hypersecretion, and AHR. We have identified novel roles for tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) and IL-13 in promoting infection-induced pathology in early life and subsequent chronic lung disease. Genetic deletion of TRAIL or IL-13 variously protected against neonatal infection-induced inflammation, mucus hypersecretion, altered lung structure, AHR, and impaired lung function. Therapeutic neutralization of these factors prevented infection-induced severe AAD. Other novel mechanisms and avenues for intervention are also being explored. Such studies indicate the immunological mechanisms that may underpin the association between early-life respiratory infections and the development of more severe asthma and may facilitate the development of tailored preventions and treatments.

Harasti, D, Martin-Smith, K & Gladstone, W 2014, 'Does a No-Take Marine Protected Area Benefit Seahorses?', PLoS ONE, vol. 9, no. 8, pp. e105462-e105462.
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Seahorses are iconic charismatic species that are often used to `champion marine conservation causes around the world. As they are threatened in many countries by over-exploitation and habitat loss, marine protected areas (MPAs) could help with their protection and recovery. MPAs may conserve seahorses through protecting essential habitats and removing fishing pressures. Populations of White's seahorse, Hippocampus whitei, a species endemic to New South Wales, Australia, were monitored monthly from 2006 to 2009 using diver surveys at two sites within a no-take marine protected areas established in 1983, and at two control sites outside the no-take MPA sites. Predators of H. whitei were also identified and monitored. Hippocampus whitei were more abundant at the control sites. Seahorse predators (3 species of fish and 2 species of octopus) were more abundant within the no-take MPA sites. Seahorse and predator abundances were negatively correlated. Substantial variability in the seahorse population at one of the control sites reinforced the importance of long-term monitoring and use of multiple control sites to assess the outcomes of MPAs for seahorses. MPAs should be used cautiously to conserve seahorse populations as there is the risk of a negative impact through increased predator abundance.

Harasti, D, Martin‐Smith, K & Gladstone, W 2014, 'Ontogenetic and sex‐based differences in habitat preferences and site fidelity of White's seahorse Hippocampus whitei', Journal of Fish Biology, vol. 85, no. 5, pp. 1413-1428.
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The aim of this study was to determine and compare habitat preferences for male and female adult and juvenile White's seahorse Hippocampus whitei and assess their movements and site fidelity over 4 years. Data were collected from three sites along 1·5 km of estuarine shoreline in Port Stephens, New South Wales, Australia, from 2006 to 2009 using H. whitei that had been tagged with visible implant fluorescent elastomer. Relative availability of 12 habitats and habitat preferences of H. whitei was determined, based on the habitat that H. whitei used as a holdfast. Hippocampus whitei occurred in nine different habitats; adults preferred sponge and soft coral Dendronephthya australis habitats with no difference between male and female habitat preferences whilst juveniles preferred gorgonian Euplexaura sp. habitat. There was a significant preference by adults for D. australis colonies with height >40 cm and avoidance of colonies <20 cm. Neither adults nor juveniles used sand or the seagrasses Zostera muelleri subsp. capricorni and Halophila ovalis. Hippocampus whitei showed cryptic behaviour with c. 50% of adult sightings cryptic and c. 75% for juveniles with crypsis occurring predominantly in Sargassum sp. for adults and Euplexaura sp. habitat for juveniles. Within sites, females moved significantly longer distances (maximum of 70 m) than males (maximum of 38 m) over 20 months. Strong site fidelity was displayed by H. whitei with males persisting at the same site for up to 56 months and female...

Hare, DJ, George, JL, Bray, L, Volitakis, I, Vais, A, Ryan, TM, Cherny, RA, Bush, AI, Masters, CL, Adlard, PA, Doble, PA & Finkelstein, DI 2014, 'The effect of paraformaldehyde fixation and sucrose cryoprotection on metal concentration in murine neurological tissue', JOURNAL OF ANALYTICAL ATOMIC SPECTROMETRY, vol. 29, no. 3, pp. 565-570.
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Aldehyde preservation of tissue and cryoprotection by sugars and polyols has traditionally been used in histology to preserve structural integrity of samples. The effect of paraformaldehyde (PFA) fixation and sucrose cryoprotection on murine brain metals was studied by examining the changes in total brain metal levels throughout a complete fixation/cryoprotection protocol. Blank-corrected metal levels in 4% PFA and two changes of 30% sucrose solutions following brain immersion were determined by ICP-MS. Fixed and cryoprotected tissue was lyophilised, digested in HNO3/H2O2 and analysed using the same ICP-MS protocol. The sum of metal loss or gain in each solution and total digest was used to determine the percentage of total brain metal present in fixed, cryoprotected tissue. Almost all K (99.78%) and Mg (78.01%) leached from brain tissue during fixation and cryoprotection, whilst Ca and Sr either retained or absorbed additional metal ions from the sucrose solution. Less water-soluble transition metals displayed smaller degrees of metal leaching, with Fe, Cu and Zn losing 26.6131.62% of their total metal content during preparation for cryosectioning. These results suggest that metal leaching is highly metal specific, and that preparatory steps for cryosectioning of brain tissue should be approached according to this specificity.

Hare, DJ, Lei, P, Ayton, S, Roberts, BR, Grimm, R, George, JL, Bishop, DP, Beavis, AD, Donovan, SJ, McColl, G, Volitakis, I, Masters, CL, Adlard, PA, Cherny, RA, Bush, AI, Finkelstein, DI & Doble, PA 2014, 'An iron-dopamine index predicts risk of parkinsonian neurodegeneration in the substantia nigra pars compacta', CHEMICAL SCIENCE, vol. 5, no. 6, pp. 2160-2169.
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The co-localization of iron and dopamine raises the risk of a potentially toxic reaction. Disturbance of the balance in this unique chemical environment makes neurons in the substantia nigra pars compacta (SNc) particularly vulnerable to parkinsonian neurodegeneration in the aging brain. In Parkinson's disease, these neurons degenerate coincident with an elevation in brain iron levels, yet relatively little is known about specific regional iron distribution with respect to dopamine. To directly appraise the irondopamine redox couple, we applied immuno-assisted laser ablation-inductively coupled plasma-mass spectrometry imaging to co-localize iron with the dopamine-producing enzyme tyrosine hydroxylase at the coronal level of the substantia nigra. We found that in the healthy brain the SNc does not contain the greatest concentration of iron within the midbrain, while the dopamine-rich environment in this region reflects an increased oxidative load. The product of iron and dopamine was significantly greater in the SNc than the adjacent ventral tegmental area, which is less susceptible to neuron loss in Parkinson's disease. Accordingly, this `risk factor was elevated further following 6-hydroxydopamine (6-OHDA) lesioning. Considering mounting evidence that brain iron increases with age, this measurable irondopamine index provides direct experimental evidence of a relationship between these two redox-active chemicals in degenerating dopaminergic neurons.

Hassler, CS, Ridgway, KR, Bowie, AR, Butler, ECV, Clementson, LA, Doblin, MA, Davies, DM, Law, C, Ralph, PJ, van der Merwe, P, Watson, R & Ellwood, MJ 2014, 'Primary productivity induced by iron and nitrogen in the Tasman Sea: an overview of the PINTS expedition', MARINE AND FRESHWATER RESEARCH, vol. 65, no. 6, pp. 517-537.
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The Tasman Sea and the adjacent Sub-Antarctic zone (SAZ) are economically important regions, where the parameters controlling the phytoplankton community composition and carbon fixation are not yet fully resolved. Contrasting nutrient distributions as well as phytoplankton biomass, biodiversity and productivity we observed between the North Tasman Sea and the SAZ. In-situ FV/FM, dissolved and particulate nutrients, iron biological uptake, and nitrogen and carbon fixation were used to determine the factor limiting phytoplankton growth and productivity in the North Tasman Sea and the SAZ. Highly productive cyanobacteria dominated the North Tasman Sea. High atmospheric nitrogen fixation and low nitrate dissolved concentrations indicated that non-diazotroph phytoplankton are nitrogen limited. Deck-board incubations also suggested that, at depth, iron could limit eukaryotes, but not cyanobacteria in that region. In the SAZ, the phytoplankton community was dominated by a bloom of haptophytes. The low productivity in the SAZ was mainly explained by light limitation, but nitrogen, silicic acid as well as iron were all depleted to the extent that they could become co-limiting. This study illustrates the challenge associated with identification of the limiting nutrient as it varied between phytoplankton groups, depths and sites.

Henschke, N, Everett, JD, Doblin, MA, Pitt, KA, Richardson, AJ & Suthers, IM 2014, 'Demography and interannual variability of salp swarms (Thalia democratica)', MARINE BIOLOGY, vol. 161, no. 1, pp. 149-163.
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Swarms of the pelagic tunicate, Thalia democratica, form during spring, but the causes of the large interannual variability in the magnitude of salp swarms are unclear. Changes in asexual reproduction (buds per chain) of T. democratica populations in the coastal waters of south-east Australia (32-35°S) were observed in three austral springs (October 2008-2010). T. democratica abundance was significantly higher in 2008 (1,312 individuals m-3) than 2009 and 2010 (210 and 92 individuals m-3, respectively). There was a significant negative relationship (linear regression, r 2 = 0.61, F 1,22 = 33.83, P < 0.001) between abundance and asexual reproduction. Similarly, relative growth rates declined with decreasing abundance. Generalised additive mixed modelling showed that T. democratica abundance was significantly positively related to preferred food >2 μm in size (P < 0.05) and negatively related to the proportion of non-salp zooplankton (P < 0.001). Salp swarm magnitude, growth, and asexual reproduction may depend on the abundance of larger phytoplankton (prymnesiophytes and diatoms) and competition with other zooplankton. © 2013 Springer-Verlag Berlin Heidelberg.

Henschke, N, Everett, JD, Doblin, MA, Pitt, KA, Richardson, AJ & Suthers, IM 2014, 'Demography and interannual variability of salp swarms (Thalia democratica)', Marine Biology, vol. 161, no. 1, pp. 149-163.
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Herbert, C, Zeng, Q-X, Shanmugasundaram, R, Garthwaite, L, Oliver, BG & Kumar, RK 2014, 'Response of airway epithelial cells to double-stranded RNA in an allergic environment', Translational Respiratory Medicine, vol. 2, no. 1, pp. 11-11.
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AbstractBackgroundRespiratory viral infections are the most common trigger of acute exacerbations in patients with allergic asthma. The anti-viral response of airway epithelial cells (AEC) may be impaired in asthmatics, while cytokines produced by AEC may drive the inflammatory response. We investigated whether AEC cultured in the presence of Th2 cytokines associated with an allergic environment exhibited altered responses to double-stranded RNA, a virus-like stimulus.MethodsWe undertook preliminary studies using the MLE-12 cell line derived from mouse distal respiratory epithelial cells, then confirmed and extended our findings using low-passage human AEC. Cells were cultured in the absence or presence of the Th2 cytokines IL-4 and IL-13 for 48 hours, then stimulated with poly I:C for 4 hours. Expression of relevant anti-viral response and cytokine genes was assessed by quantitative real-time PCR. Secretion of cytokine proteins was assessed by immunoassay.ResultsFollowing stimulation with poly I:C, MLE-12 cells pre-treated with Th2 cytokines exhibited significantly higher levels of expression of mRNA for the cytokine genesCxcl10andCxcl11, as well as a trend towards increased expression ofCxcl9andIl6.Expression of anti-viral response genes was mostly unchanged, althoughStat1, Ifit1andIfitm3were significantly increased in Th2 cytokine pre-treated cells. Human AEC pre-treated with IL-4 and IL-13, then stimulated with poly I:C, similarly exhibited significantly higher expression ofIL8, CXCL9, CXCL10, CXCL11andCCL5genes. In parallel, there was significant...

Herron, GA, Langfield, BJ, Bogema, DR & Chen, Y 2014, 'Baseline susceptibility and cross-resistance in Aphis gossypii Glover (Aphididae: Hemiptera) to phorate and sulfoxaflor', AUSTRAL ENTOMOLOGY, vol. 53, no. 1, pp. 32-35.
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Susceptible discriminating doses of phorate (0.2 g/L) and sulfoxaflor (0.01 g/L) against cotton aphid Aphis gossypii Glover were determined by laboratory bioassay where aphids were sprayed with insecticide with the aid of a Potter spray tower. All of the populations tested were susceptible to sulfoxaflor, and only a pirimicarb resistant strain had cross-resistance to phorate. If phorate is used as a side dressing in Australian cotton for insect control, neither pirimicarb, or any other chemical associated with insensitive acetylcholinesterase type one resistance, should be used as the first foliar spray for any subsequent aphid control.

Heselmeyer-Haddad, KM, Berroa Garcia, LY, Bradley, A, Hernandez, L, Hu, Y, Habermann, JK, Dumke, C, Thorns, C, Perner, S, Pestova, E, Burke, C, Chowdhury, SA, Schwartz, R, Schäffer, AA, Paris, PL & Ried, T 2014, 'Single-Cell Genetic Analysis Reveals Insights into Clonal Development of Prostate Cancers and Indicates Loss of PTEN as a Marker of Poor Prognosis', The American Journal of Pathology, vol. 184, no. 10, pp. 2671-2686.
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Hill, R, Szabo, M, Rehman, AU, Vass, I, Ralph, PJ & Larkum, AWD 2014, 'Inhibition of photosynthetic CO2 fixation in the coral Pocillopora damicornis and its relationship to thermal bleaching', JOURNAL OF EXPERIMENTAL BIOLOGY, vol. 217, no. 12, pp. 2150-2162.
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© 2014. Published by The Company of Biologists Ltd. Two inhibitors of the Calvin-Benson cycle [glycolaldehyde (GA) and potassium cyanide (KCN)] were used in cultured Symbiodinium cells and in nubbins of the coral Pocillopora damicornis to test the hypothesis that inhibition of the Calvin-Benson cycle triggers coral bleaching. Inhibitor concentration range-finding trials aimed to determine the appropriate concentration to generate inhibition of the Calvin-Benson cycle, but avoid other metabolic impacts to the symbiont and the animal host. Both 3 mmol l-1 GA and 20 uμmol l-1 KCN caused minimal inhibition of host respiration, but did induce photosynthetic impairment, measured by a loss of photosystem II function and oxygen production. GA did not affect the severity of bleaching, nor induce bleaching in the absence of thermal stress, suggesting inhibition of the Calvin-Benson cycle by GA does not initiate bleaching in P. damicornis. In contrast, KCN did activate a bleaching response through symbiont expulsion, which occurred in the presence and absence of thermal stress. While KCN is an inhibitor of the Calvin-Benson cycle, it also promotes reactive oxygen species formation, and it is likely that this was the principal agent in the coral bleaching process. These findings do not support the hypothesis that temperature-induced inhibition of the Calvin-Benson cycle alone induces coral bleaching.

Hirota, JA, Alexis, NE, Pui, M, Wong, S, Fung, E, Hansbro, P, Knight, DA, Sin, DD & Carlsten, C 2014, 'PM10‐stimulated airway epithelial cells activate primary human dendritic cells independent of uric acid: Application of an in vitro model system exposing dendritic cells to airway epithelial cell‐conditioned media', Respirology, vol. 19, no. 6, pp. 881-890.
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AbstractBackground and objectiveAirway epithelial cells represent the first line of defence against inhaled insults, including air pollution. Air pollution can activate innate immune signalling in airway epithelial cells leading to the production of soluble mediators that can influence downstream inflammatory cells. Our objective was to develop and validate a model of dendritic cell exposure to airway epithelial cell‐conditioned media. After establishing the model, we explored how soluble mediators released from airway epithelial cells in response to air pollution influenced the phenotype of dendritic cells.MethodsHuman airway epithelial cells were cultured under control and urban particulate matter (PM10) exposure conditions with or without pharmacological inhibitors of the uric acid pathway. Culture supernatants were collected for conditioned media experiments with peripheral blood mononuclear cell‐derived dendritic cells analysed by flow cytometry.ResultsMonocytes derived from peripheral blood mononuclear cells cultured in interleukin‐4 and granulocyte macrophage colony stimulating factor differentiated into immature dendritic cells that phenotypically differentiated into mature dendritic cells in response to conditioned media from phorbol myristate acetate‐activated THP‐1 monocytes. Exposure of immature dendritic cells to conditioned media from airway epithelial cells exposed to PM10 resulted in dendritic cell maturation that was independent of uric acid.ConclusionsWe present a conditioned media model useful for in...

Ho, KKK, Chen, R, Willcox, MDP, Rice, SA, Cole, N, Iskander, G & Kumar, N 2014, 'Quorum sensing inhibitory activities of surface immobilized antibacterial dihydropyrrolones via click chemistry', Biomaterials, vol. 35, no. 7, pp. 2336-2345.
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Hoe, M & Nicholas, HR 2014, 'Evidence of a MOF histone acetyltransferase-containing NSL complex inC. elegans', Worm, vol. 3, no. 4, pp. e982967-e982967.
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Regulation of chromatin is a key process in the developmental control of gene expression. Many multi-subunit protein complexes have been found to regulate chromatin through the modification of histone residues. One such complex is the MOF histone acetyltransferase-containing NSL complex. While the composition of the human and Drosophila NSL complexes has been determined and the functions of these complexes investigated, the existence of an equivalent complex in nematodes such as Caenorhabditis elegans has not yet been explored. Here we summarise evidence, from our own work and that of others, that homologues of NSL complex components are found in C. elegans. We review data suggesting that nematode proteins SUMV-1 and SUMV-2 are homologous to NSL2 and NSL3, respectively, and that SUMV-1 and SUMV-2 may form a complex with MYS-2, the worm homolog of MOF. We propose that these interactions suggest the existence of a nematode NSL-like complex and discuss the roles of this putative NSL complex in worms as well as exploring the possibility of crosstalk between NSL and COMPASS complexes via components that are common to both. We present the groundwork from which a full characterization of a nematode NSL complex may begin.

Hoiles, W, Krishnamurthy, V, Cranfield, CG & Cornell, B 2014, 'An Engineered Membrane to Measure Electroporation: Effect of Tethers and Bioelectronic Interface', BIOPHYSICAL JOURNAL, vol. 107, no. 6, pp. 1339-1351.
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© 2014 by the Biophysical Society. This article reports on the construction and predictive models for a platform comprised of an engineered tethered membrane. The platform provides a controllable and physiologically relevant environment for the study of the electroporation process. The mixed self-assembled membrane is formed via a rapid solvent exchange technique. The membrane is tethered to the gold electrode and includes an ionic reservoir separating the membrane and gold surface. Above the membrane, there is an electrolyte solution, and a gold counterelectrode. A voltage is applied between the gold electrodes and the current measured. The current is dependent on the energy required to form aqueous pores and the conductance of each pore. A two-level predictive model, consisting of a macroscopic and a continuum model, is developed to relate the pore dynamics to the measured current. The macroscopic model consists of an equivalent circuit model of the tethered membrane, and asymptotic approximations to the Smoluchowski-Einstein equation of electroporation that is dependent on the pore conductance and the energy required to form aqueous pores. The continuum model is a generalized Poisson-Nernst-Planck (GPNP) system where an activity coefficient to account for steric effects of ions is added to the standard PNP system. The GPNP is used to evaluate the conductance of aqueous pores, and the electrical energy required to form the pores. As an outcome of the setup of the device and the two-level model, biologically important variables can be estimated from experimental measurements. To validate the accuracy of the two-level model, the predicted current is compared with experimentally measured current for different tethering densities.

Hu, K, Kabakova, IV, Büttner, TFS, Lefrancois, S, Hudson, DD, He, S & Eggleton, BJ 2014, 'Low-threshold Brillouin laser at 2  μm based on suspended-core chalcogenide fiber', Optics Letters, vol. 39, no. 16, pp. 4651-4651.
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We present, to the best of our knowledge, the first demonstration of a 2 μm Brillouin laser based on a thulium-doped fiber pump and a chalcogenide fiber. A short 1.5mpiece of suspended-core chalcogenide As38Se 62 fiber is employed as a gain medium, taking advantage of its small effective mode area and high Brillouin gain coefficient. A record-low lasing threshold of 52 mW is achieved, which is about 10 times lower than previously demonstrated in silica fiber cavities. © 2014 Optical Society of America.

Hu, K, Kabakova, IV, Lefrancois, S, Hudson, DD, He, S & Eggleton, BJ 2014, 'Hybrid Brillouin/thulium multiwavelength fiber laser with switchable single- and double-Brillouin-frequency spacing', Optics Express, vol. 22, no. 26, pp. 31884-31884.
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Huang, X, Sun, B, Chen, S & Wang, G 2014, 'Self-Assembling Synthesis of Free-standing Nanoporous Graphene-Transition-Metal Oxide Flexible Electrodes for High-Performance Lithium-Ion Batteries and Supercapacitors', CHEMISTRY-AN ASIAN JOURNAL, vol. 9, no. 1, pp. 206-211.
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The synthesis of nanoporous graphene by a convenient carbon nanofiber assisted self-assembly approach is reported. Porous structures with large pore volumes, high surface areas, and well-controlled pore sizes were achieved by employing spherical silica as hard templates with different diameters. Through a general wet-immersion method, transition-metal oxide (Fe3O 4, Co3O4, NiO) nanocrystals can be easily loaded into nanoporous graphene papers to form three-dimensional flexible nanoarchitectures. When directly applied as electrodes in lithium-ion batteries and supercapacitors, the materials exhibited superior electrochemical performances, including an ultra-high specific capacity, an extended long cycle life, and a high rate capability. In particular, nanoporous Fe3O 4-graphene composites can deliver a reversible specific capacity of 1427.5 mAh g-1 at a high current density of 1000 mA g-1 as anode materials in lithium-ion batteries. Furthermore, nanoporous Co 3O4-graphene composites achieved a high supercapacitance of 424.2 F g-1. This work demonstrated that the as-developed freestanding nanoporous graphene papers could have significant potential for energy storage and conversion applications. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Huang, X, Sun, B, Su, D, Zhao, D & Wang, G 2014, 'Soft-template synthesis of 3D porous graphene foams with tunable architectures for lithium-O-2 batteries and oil adsorption applications', JOURNAL OF MATERIALS CHEMISTRY A, vol. 2, no. 21, pp. 7973-7979.
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We report a general emulsion soft-template method to synthesize porous graphene foams for multi-functional applications, including lithium-oxygen batteries and oil-adsorption. Multiple micro-emulsions and micelles were employed to produce three-dimensional porous graphene with well-tailored inter-architecture for the first time. Detailed mechanism study reveals that specific interfacial interactions, such as π-π interaction, hydrophobic affinity or electrostatic interaction, are vital for the formation of porous graphene materials. When applied as cathode materials in lithium-oxygen batteries, the porous graphene foams exhibited good catalytic activity. Besides, the porous graphene materials also demonstrated the capability for oil adsorption with a high efficiency. This journal is © the Partner Organisations 2014.

Huang, X, Zhao, Y, Ao, Z & Wang, G 2014, 'Micelle-Template Synthesis of Nitrogen-Doped Mesoporous Graphene as an Efficient Metal-Free Electrocatalyst for Hydrogen Production', Scientific Reports, vol. 4, no. 1.
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Synthesis of mesoporous graphene materials by softlate methods remains a great challenge, owing to the poor self-assembly capability of precursors and the severe agglomeration of graphene nanosheets. Herein, a micellelate strategy to prepare porous graphene materials with controllable mesopores, high specific surface areas and large pore volumes is reported. By fine-tuning the synthesis parameters, the pore sizes of mesoporous graphene can be rationally controlled. Nitrogen heteroatom doping is found to remarkably render electrocatalytic properties towards hydrogen evolution reactions as a highly efficient metal-free catalyst. The synthesis strategy and the demonstration of highly efficient catalytic effect provide benchmarks for preparing well-defined mesoporous graphene materials for energy production applications.

Huang, Y, Hu, D, Wen, S, Shen, M, Zhu, M & Shi, X 2014, 'Selective removal of mercury ions using thymine-grafted electrospun polymer nanofibers', NEW JOURNAL OF CHEMISTRY, vol. 38, no. 4, pp. 1533-1539.
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Hughes, AV, Holt, SA, Daulton, E, Soliakov, A, Charlton, TR, Roser, SJ & Lakey, JH 2014, 'High coverage fluid-phase floating lipid bilayers supported by ω-thiolipid self-assembled monolayers', Journal of The Royal Society Interface, vol. 11, no. 98, pp. 20140447-20140447.
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Large area lipid bilayers, on solid surfaces, are useful in physical studies of biological membranes. It is advantageous to minimize the interactions of these bilayers with the substrate and this can be achieved via the formation of a floating supported bilayer (FSB) upon either a surface bound phospholipid bilayer or monolayer. The FSB's independence is enabled by the continuous water layer (greater than 15 Å) that remains between the two. However, previous FSBs have had limited stability and low density. Here, we demonstrate by surface plasmon resonance and neutron reflectivity, the formation of a complete self-assembled monolayer (SAM) on gold surfaces by a synthetic phosphatidylcholine bearing a thiol group at the end of one fatty acyl chain. Furthermore, a very dense FSB (more than 96%) of saturated phosphatidylcholine can be formed on this SAM by sequential Langmuir–Blodgett and Langmuir–Schaefer procedures. Neutron reflectivity used both isotopic and magnetic contrast to enhance the accuracy of the data fits. This system offers the means to study transmembrane proteins, membrane potential effects (using the gold as an electrode) and even model bacterial outer membranes. Using unsaturated phosphatidylcholines, which have previously failed to form stable FSBs, we achieved a coverage of 73%.

Hui, JGK, Mai-Prochnow, A, Kjelleberg, S, McDougald, D & Rice, SA 2014, 'Environmental cues and genes involved in establishment of the superinfective Pf4 phage of Pseudomonas aeruginosa', Frontiers in Microbiology, vol. 5, no. DEC, pp. 1-8.
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© 2014 Hui, Mai-Prochnow, Kjelleberg, McDougald and Rice. Biofilm development in Pseudomonas aeruginosa is in part dependent on a filamentous phage, Pf4, which contributes to biofilm maturation, cell death, dispersal and variant formation, e.g., small colony variants (SCVs). These biofilm phenotypes correlate with the conversion of the Pf4 phage into a superinfection (SI) variant that reinfects and kills the prophage carrying host, in contrast to other filamentous phage that normally replicate without killing their host. Here we have investigated the physiological cues and genes that may be responsible for this conversion. Flow through biofilms typically developed SI phage approximately days 4 or 5 of development and corresponded with dispersal. Starvation for carbon or nitrogen did not lead to the development of SI phage. In contrast, exposure of the biofilm to nitric oxide, H2O2 or the DNA damaging agent, mitomycin C, showed a trend of increased numbers of SI phage, suggesting that reactive oxygen or nitrogen species (RONS) played a role in the formation of SI phage. In support of this, mutation of oxyR, the major oxidative stress regulator in P. aeruginosa, resulted in higher level of and earlier superinfection compared to the wild-type (WT). Similarly, inactivation of mutS, a DNA mismatch repair gene, resulted in the early appearance of the SI phage and this was four log higher than the WT. In contrast, loss of recA, which is important for DNA repair and the SOS response, also resulted in a delayed and decreased production of SI phage. Treatments or mutations that increased superinfection also correlated with an increase in the production of morphotypic variants. The results suggest that the accumulation of RONS by the biofilm may result in DNA lesions in the Pf4 phage, leading to the formation of SI phage, which subsequently selects for morphotypic variants, such as SCVs.

Hunt, NH, Ball, HJ, Hansen, AM, Khaw, LT, Guo, J, Bakmiwewa, S, Mitchell, AJ, Combes, VR & Grau, GER 2014, 'Cerebral malaria: gamma-interferon redux', Frontiers in Cellular and Infection Microbiology, vol. 4, no. AUG, pp. 1-12.
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There are two theories that seek to explain the pathogenesis of cerebral malaria, the mechanical obstruction hypothesis and the immunopathology hypothesis. Evidence consistent with both ideas has accumulated from studies of the human disease and experimental models. Thus, some combination of these concepts seems necessary to explain the very complex pattern of changes seen in cerebral malaria. The interactions between malaria parasites, erythrocytes, the cerebral microvascular endothelium, brain parenchymal cells, platelets and microparticles need to be considered. One factor that seems able to knit together much of this complexity is the cytokine interferon-gamma (IFN-?). In this review we consider findings from the clinical disease, in vitro models and the murine counterpart of human cerebral malaria in order to evaluate the roles played by IFN-? in the pathogenesis of this often fatal and debilitating condition. © 2014 Hunt, Ball, Hansen, Khaw, Guo, Bakmiwewa, Mitchell, Combes and Grau.

Huque, MH, Bondell, HD & Ryan, L 2014, 'On the impact of covariate measurement error on spatial regression modelling', ENVIRONMETRICS, vol. 25, no. 8, pp. 560-570.
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Hutchinson, AT, Jones, DR, McCauley Winter, P, Tangye, SG & Raison, RL 2014, 'Cell membrane associated free kappa light chains are found on a subset of tonsil and in vitro-derived plasmablasts', Human Immunology, vol. 75, no. 9, pp. 986-990.
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Idrees, S 2014, 'Clinical Application of Nursing Theory into Practice', i-manager’s Journal on Nursing, vol. 4, no. 1, pp. 23-27.
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Idrees, S & Ashfaq, UA 2014, 'Discovery and design of cyclic peptides as dengue virus inhibitors through structure-based molecular docking', Asian Pacific Journal of Tropical Medicine, vol. 7, no. 7, pp. 513-516.
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Idrees, S, Ashfaq, UA, Masoud, MS, Qasim, M, Javed, T & Ali, A 2014, 'Gene Expression Profiling of Immune Responsive and Fibrosis Genes in Hepatitis C Virus Infected Patients', Viral Immunology, vol. 27, no. 5, pp. 250-254.
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Im, H & Ammit, AJ 2014, 'The NLRP3 inflammasome: role in airway inflammation', Clinical & Experimental Allergy, vol. 44, no. 2, pp. 160-172.
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SummaryAsthma is characterized by airway inflammation, airway hyperresponsiveness and airway remodelling. Uncontrolled airway inflammation or repeated asthma exacerbations can lead to airway remodelling, which cannot be reversed by current pharmacological treatment, and consequently lead to decline in lung function. Thus, it is critical to understand airway inflammation in asthma and infectious exacerbation. The inflammasome has emerged as playing a key role in innate immunity and inflammation. Upon ligand sensing, inflammasome components assemble and self‐oligomerize, leading to caspase‐1 activation and maturation of pro‐IL‐1β and pro‐IL‐18 into bioactive cytokines. These bioactive cytokines then play a pivotal role in the initiation and amplification of inflammatory processes. In addition to facilitating the proteolytic activation of IL‐1β and IL‐18, inflammasomes also participate in cell death through caspase‐1‐mediated pyroptosis. In this review, we describe the structure and function of the inflammasome and provide an overview of our current understanding of role of the inflammasome in airway inflammation. We focus on nucleotide‐binding domain and leucine‐rich repeat protein 3 (NLRP3) inflammasome as it is the best‐characterized subtype shown expressed in airway and considered to play a key role in chronic airway diseases such as asthma.

Jaffar, J, Unger, S, Corte, TJ, Keller, M, Wolters, PJ, Richeldi, L, Cerri, S, Prêle, CM, Hansbro, PM, Argraves, WS, Oliver, RA, Oliver, BG, Black, JL & Burgess, JK 2014, 'Fibulin-1 Predicts Disease Progression in Patients With Idiopathic Pulmonary Fibrosis', CHEST, vol. 146, no. 4, pp. 1055-1063.
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Background The underlying mechanisms of idiopathic pulmonary fibrosis (IPF) are unknown. This progressive disease has high mortality rates and current models for prediction of mortality have limited value in identifying which patients will progress. We previously showed that the glycoprotein fibulin-1 is involved in enhanced proliferation and wound repair by mesenchymal cells, thus may contribute to lung fibrosis in IPF. Methods Serum, lung tissue and lung function values were obtained from four independent locations (Sydney and Perth, Australia, San Francisco, USA and Modena, Italy). Patients with IPF were followed for a minimum of one year and progression was defined as a significant decline in lung function or death. Primary parenchymal lung fibroblasts of 15 patients with and without IPF were cultured under non-stimulatory conditions. Fibulin-1 levels in serum and secreted or deposited by fibroblasts were measured by western blot and in lung tissue by immunohistochemistry. Results Serum fibulin-1 levels were increased in patients with IPF compared to subjects without lung disease (p=0.006). Furthermore, tissue fibulin-1 levels were increased in patients with IPF (p=0.02) and correlated negatively with lung function (r=-0.9, p<0.05). Primary parenchymal fibroblasts from patients with IPF produced more fibulin-1 than those from subjects without IPF (p<0.05). Finally, serum fibulin-1 levels at first blood draw predicted disease progression in IPF within 1 year (AUC 0.71, 95%CI 0.57 0.86, p=0.012). Conclusions Fibulin-1 is a novel potential biomarker for disease progression IPF and raise the possibility that it could be used as a target for the development of new treatments.

Jardine, TD, Hadwen, WL, Hamilton, SK, Hladyz, S, Mitrovic, SM, Kidd, KA, Tsoi, WY, Spears, M, Westhorpe, DP, Fry, VM, Sheldon, F & Bunn, SE 2014, 'UNDERSTANDING AND OVERCOMING BASELINE ISOTOPIC VARIABILITY IN RUNNING WATERS', RIVER RESEARCH AND APPLICATIONS, vol. 30, no. 2, pp. 155-165.
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Natural abundances of stable isotopes in lotic food webs yield valuable information about sources of organic matter for consumers and trophic structure. However, interpretation of isotopic information can be challenging in the face of variability in organisms at the base of food webs. Unionid and dreissenid mussels, commonly used as baseline organisms in lakes, are uncommon in many river settings and can have variable diets, thus making them unsuitable as a universal baseline for many river food web studies and often forcing reliance on more common benthic insects for this purpose. Turnover rates of body carbon and nitrogen in insects are relatively rapid (1 to 50 days half-life). These rapid turnover rates in primary consumers can result in considerable temporal variability in d13C that rivals that of algae (>10%range within a site). This suggests that using primary consumers as a surrogate baseline for algae may not circumvent the problem of temporal variability and the resultant mismatch of sources with longer-lived, slow-growing secondary and tertiary consumers. There are several strategies for reducing the influence of these confounding factors when bivalves with a known diet are not present. These include sampling over large spatial scales and correlating d13C of consumers with the source of interest (e.g. benthic algae), sampling baseline organisms multiple times in the weeks preceding sampling of larger consumers (particularly in response to large changes in discharge) and using algal-detrital separation methods and multiple tracers as much as possible. Incorporating some of these recommendations and further exploring variability at the base of the food web will potentially provide greater insights into consumerresource coupling in running waters and more robust conclusions about food web structure and energy flow in these dynamic systems.

Jaron, KS, Moravec, JC & Martínková, N 2014, 'SigHunt: horizontal gene transfer finder optimized for eukaryotic genomes', Bioinformatics, vol. 30, no. 8, pp. 1081-1086.
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Abstract Motivation: Genomic islands (GIs) are DNA fragments incorporated into a genome through horizontal gene transfer (also called lateral gene transfer), often with functions novel for a given organism. While methods for their detection are well researched in prokaryotes, the complexity of eukaryotic genomes makes direct utilization of these methods unreliable, and so labour-intensive phylogenetic searches are used instead. Results: We present a surrogate method that investigates nucleotide base composition of the DNA sequence in a eukaryotic genome and identifies putative GIs. We calculate a genomic signature as a vector of tetranucleotide (4-mer) frequencies using a sliding window approach. Extending the neighbourhood of the sliding window, we establish a local kernel density estimate of the 4-mer frequency. We score the number of 4-mer frequencies in the sliding window that deviate from the credibility interval of their local genomic density using a newly developed discrete interval accumulative score (DIAS). To further improve the effectiveness of DIAS, we select informative 4-mers in a range of organisms using the tetranucleotide quality score developed herein. We show that the SigHunt method is computationally efficient and able to detect GIs in eukaryotic genomes that represent non-ameliorated integration. Thus, it is suited to scanning for change in organisms with different DNA composition. Availability and implementation: Source code and scripts freely available for download at http://www.iba.muni.cz/index-en.php?pg=research–data-analysis-tools–sighunt are implemented in C and R and are platform-independent. Contact:  376090@mail.muni.cz or martinkova@ivb.cz

Jeans, J, Szabo, M, Campbell, DA, Larkum, AWD, Ralph, PJ & Hill, R 2014, 'Thermal bleaching induced changes in photosystem II function not reflected by changes in photosystem II protein content of Stylophora pistillata', CORAL REEFS, vol. 33, no. 1, pp. 131-139.
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Scleractinian corals exist in a symbiosis with marine dinoflagellates of the genus Symbiodinium that is easily disrupted by changes in the external environment. Increasing seawater temperatures cause loss of pigments and expulsion of the symbionts from the host in a process known as coral bleaching; though, the exact mechanism and trigger of this process has yet to be elucidated. We exposed nubbins of the coral Stylophora pistillata to bleaching temperatures over a period of 14 daylight hours. Fifty-nine percent of the symbiont population was expelled over the course of this short-term treatment. Maximum quantum yield (F V/F M) of photosystem (PS) II for the in hospite symbiont population did not change significantly over the treatment period, but there was a significant decline in the quantity of PSII core proteins (PsbA and PsbD) at the onset of the experimental increase in temperature. F V/F M from populations of expelled symbionts dropped sharply over the first 6 h of temperature treatment, and then toward the end of the experiment, it increased to an F V/F M value similar to that of the in hospite population. This suggests that the symbionts were likely damaged prior to expulsion from the host, and the most damaged symbionts were expelled earlier in the bleaching. The quantity of PSII core proteins, PsbA and PsbD, per cell was significantly higher in the expelled symbionts than in the remaining in hospite population over 6-10 h of temperature treatment. We attribute this to a buildup of inactive PSII reaction centers, likely caused by a breakdown in the PSII repair cycle. Thus, thermal bleaching of the coral S. pistillata induces changes in PSII content that do not follow the pattern that would be expected based on the results of PSII function. © 2013 Springer-Verlag Berlin Heidelberg.

Jelinek, L, Lapine, M & McPhedran, RC 2014, 'Applicability of nonresonant artificial diamagnetics', PHYSICAL REVIEW B, vol. 90, no. 10, pp. 104413-1-104413-5.
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© 2014 American Physical Society. Artificial diamagnetics are prominent for achieving extraordinarily strong diamagnetism in a wide frequency range. However, as far as the magnetic fields outside the artificial medium are concerned, bulk conductors show a very similar pattern. The question arises whether the complicated internal structure of artificial diamagnetics can, to this end, be replaced by a simpler object. We show that for an electrically small body, internal structuring is likely to make the effective diamagnetic response weaker than that of a simple conducting object.

Jeong, S, Rice, SA & Vigneswaran, S 2014, 'Long-term effect on membrane fouling in a new membrane bioreactor as a pretreatment to seawater desalination', Bioresource Technology, vol. 165, no. C, pp. 60-68.
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© 2014 Elsevier Ltd. Submerged membrane adsorption bio-reactors (SMABR) were investigated as a new pretreatment for seawater reverse osmosis (SWRO) desalination. They were tested with different doses of powder activated carbon (PAC) on-site for a long-term. The biofouling on the membrane was assessed in terms of DNA (cells) and polysaccharide distribution. MBR without PAC addition resulted in severe fouling on membrane. When PAC is added in the MBR, PAC could reduce the organic fouling. Hence the biofilm formation on membrane was reduced without any membrane damage. PAC also helped to remove low molecular weight (LMW) organics responsible for biofouling of RO membrane. A linear correlation between assimilable organic carbon (AOC) and LMW organics was observed. A small amount of PAC (2.4-8.0g of PAC/m3 of seawater) was sufficient to reduce biofouling. It indicated that SMABR is an environmentally-friendly biological pretreatment to reduce biofouling for SWRO.

Jessop, TS, Dempster, T, Letnic, M & Webb, JK 2014, 'Interplay among nocturnal activity, melatonin, corticosterone and performance in the invasive cane toad (Rhinella marinus)', GENERAL AND COMPARATIVE ENDOCRINOLOGY, vol. 206, pp. 43-50.
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Most animals conduct daily activities exclusively either during the day or at night. Here, hormones such as melatonin and corticosterone, greatly influence the synchronization or regulation of physiological and behavioral cycles needed for daily activity. How then do species that exhibit more flexible daily activity patterns, responses to ecological, environmental or life-history processes, regulate daily hormone profiles important to daily performance? This study examined the consequences of (1) nocturnal activity on diel profiles of melatonin and corticosterone and (2) the effects of experimentally increased acute melatonin levels on physiological and metabolic performance in the cane toad (Rhinella marinus). Unlike inactive captive toads that had a distinct nocturnal melatonin profile, nocturnally active toads sampled under field and captive conditions, exhibited decreased nocturnal melatonin profiles with no evidence for any phase shift. Nocturnal corticosterone levels were significantly higher in field active toads than captive toads. In toads with experimentally increased melatonin levels, plasma lactate and glucose responses following recovery post exercise were significantly different from control toads. However, exogenously increased melatonin did not affect resting metabolism in toads. These results suggest that toads could adjust daily hormone profiles to match nocturnal activity requirements, thereby avoiding performance costs induced by high nocturnal melatonin levels. The ability of toads to exhibit plasticity in daily hormone cycles, could have broad implications for how they and other animals utilize behavioral flexibility to optimize daily activities in response to natural and increasingly human mediated environmental variation. © 2014 Elsevier Inc.

Jiang, L, Phang, JM, Yu, J, Harrop, SJ, Sokolova, AV, Duff, AP, Wilk, KE, Alkhamici, H, Breit, SN, Valenzuela, SM, Brown, LJ & Curmi, PMG 2014, 'CLIC proteins, ezrin, radixin, moesin and the coupling of membranes to the actin cytoskeleton: A smoking gun?', BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, vol. 1838, no. 2, pp. 643-657.
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The CLIC proteins are a highly conserved family of metazoan proteins with the unusual ability to adopt both soluble and integral membrane forms. The physiological functions of CLIC proteins may include enzymatic activity in the soluble form and anion channel activity in the integral membrane form. CLIC proteins are associated with the ERM proteins: ezrin, radixin and moesin. ERM proteins act as cross-linkers between membranes and the cortical actin cytoskeleton. Both CLIC and ERM proteins are controlled by Rho family small GTPases. CLIC proteins, ERM and Rho GTPases act in a concerted manner to control active membrane processes including the maintenance of microvillar structures, phagocytosis and vesicle trafficking. All of these processes involve the interaction of membranes with the underlying cortical actin cytoskeleton. The relationships between Rho GTPases, CLIC proteins, ERM proteins and the membrane:actin cytoskeleton interface are reviewed. Speculative models are proposed involving the formation of localised multi-protein complexes on the membrane surface that assemble via multiple weak interactions. This article is part of a Special Issue entitled: Reciprocal influences between cell cytoskeleton and membrane channels, receptors and transporters

John Harkness, JE 2014, 'Update on the Molecular Epidemiology and Diagnostic Tools for Blastocystis sp', Journal of Medical Microbiology & Diagnosis, vol. 03, no. 01.
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John, U, Litaker, RW, Montresor, M, Murray, S, Brosnahan, ML & Anderson, DM 2014, 'Formal Revision of the Alexandrium tamarense Species Complex (Dinophyceae) Taxonomy: The Introduction of Five Species with Emphasis on Molecular-based (rDNA) Classification', PROTIST, vol. 165, no. 6, pp. 779-804.
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© 2014 Elsevier GmbH. The Alexandrium tamarense species complex is one of the most studied marine dinoflagellate groups due to its ecological, toxicological and economic importance. Several members of this complex produce saxitoxin and its congeners - potent neurotoxins that cause paralytic shellfish poisoning. Isolates from this complex are assigned to A. tamarense, A. fundyense, or A. catenella based on two main morphological characters: the ability to form chains and the presence/absence of a ventral pore between Plates 1' and 4'. However, studies have shown that these characters are not consistent and/or distinctive. Further, phylogenies based on multiple regions in the rDNA operon indicate that the sequences from morphologically indistinguishable isolates partition into five clades. These clades were initially named based on their presumed geographic distribution, but recently were renamed as Groups I-V following the discovery of sympatry among some groups. In this study we present data on morphology, ITS/5.8S genetic distances, ITS2 compensatory base changes, mating incompatibilities, toxicity, the sxtA toxin synthesis gene, and rDNA phylogenies. All results were consistent with each group representing a distinct cryptic species. Accordingly, the groups were assigned species names as follows: Group I, A. fundyense; Group II, A. mediterraneum; Group III, A. tamarense; Group IV, A. pacificum; Group V, A. australiense.

Johnson, AP & Wallman, JF 2014, 'Effect of massing on larval growth rate', Forensic Science International, vol. 241, pp. 141-149.
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Johnson, AP & Wallman, JF 2014, 'Infrared imaging as a non-invasive tool for documenting maggot mass temperatures', Australian Journal of Forensic Sciences, vol. 46, no. 1, pp. 73-79.
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Johnson, AP, Wighton, SJ & Wallman, JF 2014, 'Tracking Movement and Temperature Selection of Larvae of Two Forensically Important Blow Fly Species Within a “Maggot Mass”', Journal of Forensic Sciences, vol. 59, no. 6, pp. 1586-1591.
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AbstractThe current study responds to the lack of understanding about the temperatures experienced by individual blow fly larvae within “maggot masses.” The temperature selection of both aggregating (in a mass) and nonaggregating larvae was compared and their pattern of movement assessed. Infrared imaging determined the temperatures within a mass and in the vicinity of the constituent individual larvae, whose movements were tracked by dyeing their tissues red. Individual Chrysomya rufifacies larvae selected temperatures above 27°C, significantly higher than the temperature selected by Calliphora vicina larvae (24.5°C). However, this same difference was not seen within a mass, with both species selecting temperatures around 28°C. Larval movement in a mass was nonrandom, indicating that larvae actively select their position in a mass. Furthermore, larvae have a strong tendency to select the hottest part of a mass; therefore, maximum mass temperatures might provide a reliable proxy for the actual temperatures experienced by larvae.

Johnston, RA, Rawling, T, Chan, T, Zhou, F & Murray, M 2014, 'Selective Inhibition of Human Solute Carrier Transporters by Multikinase Inhibitors', Drug Metabolism and Disposition, vol. 42, no. 11, pp. 1851-1857.
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© 2014 by The American Society for Pharmacology and Experimental Therapeutics. Solute carrier (SLC) transporters regulate the cellular influx and disposition of endogenous and xenobiotic compounds, including anticancer agents such as the multikinase inhibitors (MKIs). Recent evidence suggests that MKIs may also inhibit SLC-dependent transport of coadministered drugs, although present information on the relative susceptibilities of multiple SLC transporters is limited. This study evaluated 18 MKI drugs and metabolites as inhibitors of prototypic substrate uptake by 13 SLC transporters that were overexpressed in human embryonic kidney cells. Organic anion transporting polypeptides (OATPs) 1A2, 1B3, and 2B1, organic anion transporter 3 (OAT3), and organic cation transporter 1 (OCT1) were inhibited by most MKIs, whereas substrate uptake by OATP1B1, OAT1, 2, and 4, OCT2 and 3, and organic zwitterion/cation transporter 1 (OCTN1) was less susceptible to inhibition; OCTN2 was also inhibited by cediranib. In further studies, IC50 values were determined for the most effective MKIs, and erlotinib and cediranib were found to be potent competitive inhibitors of OATP2B1 (Ki= 41 nM) and OATP1A2 (Ki= 33 nM), respectively. From predictive approaches, several MKI-SLC interactions were found to be of potential in vivo significance. Copyright

Jones, PM & George, AM 2014, 'A reciprocating twin-channel model for ABC transporters', Quarterly Reviews of Biophysics, vol. 47, no. 3, pp. 189-220.
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AbstractABC transporters comprise a large, diverse, and ubiquitous superfamily of membrane active transporters. Their core architecture is a dimer of dimers, comprising two transmembrane (TM) domains that bind substrate, and two ATP-binding cassettes, which use the cell's energy currency to couple substrate translocation to ATP hydrolysis. Despite the availability of over a dozen resolved structures and a wealth of biochemical and biophysical data, this field is bedeviled by controversy and long-standing mechanistic questions remain unresolved. The prevailing paradigm for the ABC transport mechanism is the Switch Model, in which the ATP-binding cassettes dimerize upon binding two ATP molecules, and thence dissociate upon sequential ATP hydrolysis. This cycle of nucleotide-binding domain (NBD) dimerization and dissociation is coupled to a switch between inward- or outward facing conformations of a single TM channel; this alternating access enables substrate binding on one face of the membrane and its release at the other. Notwithstanding widespread acceptance of the Switch Model, there is substantial evidence that the NBDs do not separate very much, if at all, and thus physical separation of the ATP cassettes observed in crystallographic structures may be an artefact. An alternative Constant Contact Model has been proposed, in which ATP hydrolysis occurs alternately at the two ATP-binding sites, with one of the sites remaining closed and containing occluded nucleotide at all times. In this model, the cassettes remain in contact and the active sites swing open in an alternately seesawing motion. Whilst the concept of NBD association/dissociation in the Switch Model is naturally compatible with a single alternating-access channel, the asymmetric functioning proposed by the Constant Contact model suggests an alternating or reciprocating function in the TMDs. Here, a new model for the function of ABC transporters is proposed ...

Jones, SD, Byrne, PG & Wallman, JF 2014, 'Mating success is predicted by the interplay between multiple male and female traits in the small hairy maggot blowfly', Animal Behaviour, vol. 97, pp. 193-200.
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Kabakova, IV, Marpaung, D, Poulton, CG & Eggleton, BJ 2014, 'Driving acoustic waves optically on a chip', Australian Physics, vol. 51, no. 3, pp. 84-88.
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Stimulated Brillouin scattering (SBS) is an important nonlinear effect in optical fibers and waveguides that has been traditionally exploited for high-sensitivity distributed sensing, coherent lasers and gyroscopes. Recent advances in nanofabrication led to the extensive growth of SBS research. The ability to generate SBS in nanoscale devices has opened numerous opportunities for photonic integration, resulting in on-chip Brillouin lasers, microwave generation, Brillouin cooling and quantum optomechanics. In this paper we briefly describe principles of inelastic Brillouin scattering and review our recent developments in optical signal manipulation and lasing using on-chip SBS.

Kabakova, IV, Pant, R, Winful, HG & Eggleton, BJ 2014, 'Chalcogenide Brillouin lasers', Journal of Nonlinear Optical Physics & Materials, vol. 23, no. 01, pp. 1450001-1450001.
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In recent years, chalcogenide glasses have emerged as a material platform for nonlinear signal processing and mid-infrared photonics. In addition, high Brillouin gain of these soft glasses enable compact and highly efficient Brillouin lasers (BL). We review recent progress on chalcogenide BL, compare fiber and waveguide laser geometries, and discuss the potential of chalcogenide platform for compact and high-coherence light sources.

Kajer, TB, Fairfull-Smith, KE, Yamasaki, T, Yamada, K-I, Fu, S, Bottle, SE, Hawkins, CL & Davies, MJ 2014, 'Inhibition of myeloperoxidase- and neutrophil-mediated oxidant production by tetraethyl and tetramethyl nitroxides', FREE RADICAL BIOLOGY AND MEDICINE, vol. 70, pp. 96-105.
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The powerful oxidant HOCl (hypochlorous acid and its corresponding anion, OCl) generated by the myeloperoxidase (MPO)H2O2Cl system of activated leukocytes is strongly associated with multiple human inflammatory diseases; consequently there is considerable interest in inhibition of this enzyme. Nitroxides are established antioxidants of low toxicity that can attenuate oxidation in animal models, with this ascribed to superoxide dismutase or radical-scavenging activities. We have shown (M.D. Rees et al., Biochem. J. 421, 7986, 2009) that nitroxides, including 4-amino-TEMPO (4-amino-2,2,6,6-tetramethylpiperidin-1-yloxyl radical), are potent inhibitors of HOCl formation by isolated MPO and activated neutrophils, with IC50 values of 1 and 6 mM respectively. The utility of tetramethyl-substituted nitroxides is, however, limited by their rapid reduction by biological reductants. The corresponding tetraethyl-substituted nitroxides have, however, been reported to be less susceptible to reduction. In this study we show that the tetraethyl species were reduced less rapidly than the tetramethyl species by both human plasma (8999% decreased rate of reduction) and activated human neutrophils (6275% decreased rate). The tetraethyl-substituted nitroxides retained their ability to inhibit HOCl production by MPO and activated neutrophils with IC50 values in the low-micromolar range; in some cases inhibition was enhanced compared to tetramethyl substitution. Nitroxides with rigid structures (fused oxaspiro rings) were, however, inactive. Overall, these data indicate that tetraethyl-substituted nitroxides are potent inhibitors of oxidant formation by MPO, with longer plasma and cellular half-lives compared to the tetramethyl species, potentially allowing lower doses to be employed.

Kanazawa, A, Blanchard, GJ, Szabo, M, Ralph, PJ & Kramer, DM 2014, 'The site of regulation of light capture in Symbiodinium: Does the peridinin-chlorophyll alpha-protein detach to regulate light capture?', BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, vol. 1837, no. 8, pp. 1227-1234.
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Dinoflagellates from the genus Symbiodinium form symbiotic associations with cnidarians including corals and anemones. The photosynthetic apparatuses of these dinoflagellates possess a unique photosynthetic antenna system incorporating the peridinin-chlorophyll a-protein (PCP). It has been proposed that the appearance of a PCP-specific 77 K fluorescence emission band around 672-675 nm indicates that high light treatment results in PCP dissociation from intrinsic membrane antenna complexes, blocking excitation transfer to the intrinsic membrane-bound antenna complexes, chlorophyll a-chlorophyll c 2-peridinin-protein-complex (acpPC) and associated photosystems (Reynolds et al., 2008 Proc Natl Acad Sci USA 105:13674-13678).We have tested this model using time-resolved fluorescence decay kinetics in conjunction with global fitting to compare the time-evolution of the PCP spectral bands before and after high light exposure. Our results show that no long-lived PCP fluorescence emission components appear either before or after high light treatment, indicating that the efficiency of excitation transfer from PCP to membrane antenna systems remains efficient and rapid even after exposure to high light. The apparent increased relative emission at around 675 nm was, instead, caused by strong preferential exciton quenching of the membrane antenna complexes associated with acpPC and reaction centers. This strong non-photochemical quenching (NPQ) is consistent with the activation of xanthophyll-Associated quenching mechanisms and the generally-observed avoidance in nature of long-lived photoexcited states that can lead to oxidative damage. The acpPC component appears to be the most strongly quenched under high light exposure suggesting that it houses the photoprotective exciton quencher. © 2014 Elsevier B.V.

Kanodarwala, FK, Wang, F, Reece, PJ & Stride, JA 2014, 'Deposition of CdSe quantum dots on graphene sheets', Journal of Luminescence, vol. 146, pp. 46-52.
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High-quality TOP/TOPO capped CdSe quantum dots (QDs) displaying a narrow emission band have been grafted on to graphene nanosheets through a simple wet chemical procedure. A significant red-shift of both the broad absorption and narrow emission spectra of the QDs is induced in the resultant hybrid material, presumably by a strong graphene-QD interaction consistent with a quantum tunnelling phenomenon. The optical properties of monodisperse CdSe QDs of 3-4 nm in diameter have been determined in UV-vis and photoluminescence spectra and HRTEM and XPS data, demonstrating the successful decoration of graphene sheets with CdSe QDs. The CdSe QD absorption was observed to shift to longer wavelengths by up to 30 nm, with a corresponding shift of up to 18 nm observed in the emission band. This effect is equivalent to a narrowing of the band gap by 0.094±0.015 eV in absorption and 0.033±0.013 eV in emission, or an interaction potential of 9.1±1.5 kJ mol-1. Another is to consider the effective particle growth based upon the narrowed band gap, consistently found to be 28±1%, despite the physical size remaining unchanged. By effectively shifting the absorption and emission of CdSe QDs to longer wavelengths, this type of nanocomposite may have potential applications in the fields of optics, biological imaging and sensing. © 2013 Published by Elsevier B.V. All rights reserved.

Keast, VJ, Barnett, RL & Cortie, MB 2014, 'First principles calculations of the optical and plasmonic response of Au alloys and intermetallic compounds', JOURNAL OF PHYSICS-CONDENSED MATTER, vol. 26, no. 30.
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Keeling, PJ, Burki, F, Wilcox, HM, Allam, B, Allen, EE, Amaral-Zettler, LA, Armbrust, EV, Archibald, JM, Bharti, AK, Bell, CJ, Beszteri, B, Bidle, KD, Cameron, CT, Campbell, L, Caron, DA, Cattolico, RA, Collier, JL, Coyne, K, Davy, SK, Deschamps, P, Dyhrman, ST, Edvardsen, B, Gates, RD, Gobler, CJ, Greenwood, SJ, Guida, SM, Jacobi, JL, Jakobsen, KS, James, ER, Jenkins, B, John, U, Johnson, MD, Juhl, AR, Kamp, A, Katz, LA, Kiene, R, Kudryavtsev, A, Leander, BS, Lin, S, Lovejoy, C, Lynn, D, Marchetti, A, McManus, G, Nedelcu, AM, Menden-Deuer, S, Miceli, C, Mock, T, Montresor, M, Moran, MA, Murray, S, Nadathur, G, Nagai, S, Ngam, PB, Palenik, B, Pawlowski, J, Petroni, G, Piganeau, G, Posewitz, MC, Rengefors, K, Romano, G, Rumpho, ME, Rynearson, T, Schilling, KB, Schroeder, DC, Simpson, AGB, Slamovits, CH, Smith, DR, Smith, GJ, Smith, SR, Sosik, HM, Stief, P, Theriot, E, Twary, S, Umale, PE, Vaulot, D, Wawrik, B, Wheeler, GL, Wilson, WH, Xu, Y, Zingone, A & Worden, AZ 2014, 'The Marine Microbial Eukaryote Transcriptome Sequencing Project (MMETSP): Illuminating the Functional Diversity of Eukaryotic Life in the Oceans through Transcriptome Sequencing', PLOS BIOLOGY, vol. 12, no. 6.
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Keely, S & Hansbro, PM 2014, 'Lung-Gut Cross Talk', Chest, vol. 145, no. 2, pp. 199-200.
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Keely, S, Campbell, EL, Baird, AW, Hansbro, PM, Shalwitz, RA, Kotsakis, A, McNamee, EN, Eltzschig, HK, Kominsky, DJ & Colgan, SP 2014, 'Contribution of epithelial innate immunity to systemic protection afforded by prolyl hydroxylase inhibition in murine colitis', Mucosal Immunology, vol. 7, no. 1, pp. 114-123.
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Pharmacological stabilization of hypoxia-inducible factor (HIF) through prolyl hydroxylase (PHD) inhibition limits mucosal damage associated with models of murine colitis. However, little is known about how PHD inhibitors (PHDi) influence systemic immune function during mucosal inflammation or the relative importance of immunological changes to mucosal protection. We hypothesized that PHDi enhances systemic innate immune responses to colitis-associated bacteremia. Mice with colitis induced by trinitrobenzene sulfonic acid were treated with AKB-4924, a new HIF-1 isoform-predominant PHDi, and clinical, immunological, and biochemical endpoints were assessed. Administration of AKB-4924 led to significantly reduced weight loss and disease activity compared with vehicle controls. Treated groups were pyrexic but did not become subsequently hypothermic. PHDi treatment augmented epithelial barrier function and led to an approximately 50-fold reduction in serum endotoxin during colitis. AKB-4924 also decreased cytokines involved in pyrogenesis and hypothermia, significantly reducing serum levels of interleukin (IL)-1β, IL-6, and tumor necrosis factor (TNF)-α while increasing IL-10. Treatment offered no protection against colitis in epithelial-specific HIF-1α-deficient mice, strongly implicating epithelial HIF-1α as the tissue target for AKB-4924-mediated protection. Taken together, these results indicate that inhibition of prolyl hydroxylase with AKB-4924 enhances innate immunity and identifies that the epithelium is a central site of inflammatory protection afforded by PHDi in murine colitis. © 2014 Society for Mucosal Immunology.

Kelly, MA, Usher, MJ, Ujvari, B, Madsen, T, Wallman, JF, Buttemer, WA & Hulbert, AJ 2014, 'Diet fatty acid profile, membrane composition and lifespan: An experimental study using the blowfly (Calliphora stygia)', Mechanisms of Ageing and Development, vol. 138, pp. 15-25.
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Kendig, MD 2014, 'Cognitive and behavioural effects of sugar consumption in rodents. A review', Appetite, vol. 80, pp. 41-54.
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Kendig, MD, Ekayanti, W, Stewart, H, Boakes, RA & Rooney, KB 2014, 'Metabolic effects of access to 10% sucrose solution in female rats and transmission of some effects to their offspring', Obesity Research & Clinical Practice, vol. 8, pp. 52-53.
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Kendig, MD, Lin, CS, Beilharz, JE, Rooney, KB & Boakes, RA 2014, 'Maltodextrin can produce similar metabolic and cognitive effects to those of sucrose in the rat☆', Appetite, vol. 77, pp. 1-12.
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Kendig, MD, Rooney, KB, Corbit, LH & Boakes, RA 2014, 'Persisting adiposity following chronic consumption of 10% sucrose solution: Strain differences and behavioural effects', Physiology & Behavior, vol. 130, pp. 54-65.
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Khan, S, Fatima-Shad, K & Ghouse, HP 2014, 'Prospects of Using Platelets as Peripheral Marker to Study the Role of GABA in Autism', World Journal of Neuroscience, vol. 04, no. 05, pp. 437-442.
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Kim, J-M, Choi, M-S, Jin, B-S, Wang, G & Kim, H-S 2014, 'Physical and Electrochemical Characterization of 0.3Li<SUB>2</SUB>MnO<SUB>3</SUB>·0.7LiMn<SUB>0.60</SUB>Ni<SUB>0.25</SUB>Co<SUB>0.15</SUB>O<SUB>2</SUB> Material for Li Secondary Battery', Journal of Nanoscience and Nanotechnology, vol. 14, no. 10, pp. 7718-7722.
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The 0.3Li(2)MnO(3) center dot 0.7LiMn(0.60)Ni(0.25)Co(0.15)O(2) cathode materials were synthesized using a co-precipitation method at a various heat-treatment temperature. From XRD pattern analysis, pure layered structure without impurities was confirmed from all samples and the peak intensity of Li2MnO3 was increased as the heat-treatment temperature increased. The primary particle size increased approximately from 100 nm to 500 nm with increasing heat-treatment temperature. The initial discharge capacity of the materials obtained at 950 degrees C was 235 mA h/g at 0.1 C rate, but then decreased down to 228 mA h/g with further increasing heat-treatment temperature. And, in the voltage range of 2.0 similar to 4.6 V, the electrode heat-treated at 900 degrees C showed the highest capacity retention of 68% at 5 C rate against to 0.1 C rate.

Ko, S-K, Kim, SK, Share, A, Lynch, VM, Park, J, Namkung, W, Van Rossom, W, Busschaert, N, Gale, PA, Sessler, JL & Shin, I 2014, 'Synthetic ion transporters can induce apoptosis by facilitating chloride anion transport into cells', Nature Chemistry, vol. 6, no. 10, pp. 885-892.
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Kohan, L, Field, C, Kerr, D & Ben-Nissan, B 2014, 'Femoral neck remodelling after hip resurfacing surgery: a radiological study', ANZ Journal of Surgery, vol. 84, no. 9, pp. 639-642.
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Background: Narrowing of the femoral neck under the femoral component of the hip resurfacing has been noted previously and has raised concern. In this study we examined the X-rays of patients following Birmingham hip resurfacing surgery at 6-years follow-up. Methods: Bony changes proximally and distally were measured. Fifty-two patients were available for evaluation. Results: There were 40 (76.9%) men and 12 (23.1%) women, with a mean age of 52 years (25-64). The unoperated contralateral femoral neck was measured as a control. We found femoral neck narrowing proximally in 82.7% of patients and distally in 26.9% and on the contralateral side in 54.5%. The average narrowing was 3.6%. Widening was observed proximally in 17.3% and distally in 73.1% and on the contralateral side in 45.5%. The average widening was 3.9%. Four of the 52 patients had proximal narrowing exceeding 10% of the femoral neck diameter, and one of the 52 patients had inferior narrowing exceeding 10%. Conclusion: Gender, body mass index, component size and age did not affect remodelling. We conclude that the observed findings are likely to be a manifestation of a generalized remodelling response in the femoral neck rather than a localized and isolated narrowing at the junction of the component and the femoral neck. © 2014 Royal Australasian College of Surgeons.

Kohli, GS, Murray, SA, Neilan, BA, Rhodes, LL, Harwood, DT, Smith, KF, Meyer, L, Capper, A, Brett, S & Hallegraeff, GM 2014, 'High abundance of the potentially maitotoxic dinoflagellate Gambierdiscus carpenteri in temperate waters of New South Wales, Australia', HARMFUL ALGAE, vol. 39, pp. 134-145.
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© 2014 Elsevier B.V. Species of the genus Gambierdiscus are epiphytic dinoflagellates well known from tropical coral reef areas at water temperatures from 24 to 29°C. Gambierdiscus spp. are able to produce ciguatoxins (CTXs) known to bioaccumulate in fish, and the ingestion of tropical fish that accumulated CTXs and possibly also maitotoxins (MTXs) can cause ciguatera fish poisoning (CFP) in humans. In Australia, ciguatera poisonings have been reported in tropical parts of Queensland and the Northern Territory. Here, we report for the first time the seasonal abundance (April-May 2012/13) of Gambierdiscus spp. (up to 6565-8255cellsg-1 wet weight algae) from Merimbula and Wagonga Inlets in temperate southern New South Wales, Australia (37°S) at water temperatures of 16.5-17°C. These are popular shellfish aquaculture and recreational fisheries areas with no reports of ciguatera poisoning. Sequencing of a region of the 28S rRNA gene led to the conclusive identification of Gambierdiscus carpenteri. The cells differed however from the Belize type description, including the absence of a thecal groove, dorsal rostrum and variable hatchet- to rectangular-shaped 2' plate, and were morphologically more similar to Gambierdiscus toxicus. To study the dinoflagellate community structure in detail, a pyrosequencing approach based on the 18S rRNA gene was applied, which confirmed the presence of a single Gambierdiscus species only. Neither CTXs nor MTXs were detected in natural bloom material by LC-MS/MS; however, the extracts were found to be toxic via mouse-bioassay, with symptoms suggestive of poisoning by MTX-like compounds. Understanding the abundance of Gambierdiscus populations in areas with no apparent human health impacts is important towards defining the alternate conditions where sparse populations can create ciguatera problems.

Kohli, GS, Neilan, BA, Brown, MV, Hoppenrath, M & Murray, SA 2014, 'Cob gene pyrosequencing enables characterization of benthic dinoflagellate diversity and biogeography', ENVIRONMENTAL MICROBIOLOGY, vol. 16, no. 2, pp. 467-485.
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Dinoflagellates in marine benthic habitats living epiphytically on macroalgae are an important but highly understudied group of protists. Many produce toxins that can have severe economic impacts on marine-based economies, and improved monitoring tools are required to enhance the management of toxin-related hazards. We analysed the distribution and diversity of epibenthic dinoflagellates inhabiting eight sites in Cocos (Keeling) Islands, Papua New Guinea, and Broome and Exmouth, Western Australia. We used pyrosequencing approaches based on two DNA barcoding marker genes - 18S ribosomal RNA (rRNA) and mitochondrial cytochrome b (cob) - and compared these to an approach based on clone libraries (197 sequences) using the cob gene. Dinoflagellate sequences accounted for 133 [64 unique operational taxonomic units (OTU)] out of 10529 18S rRNA gene sequences obtained from all samples. However, using the dinoflagellate specific assay targeting the cob gene marker, we obtained 9748 (1217 unique OTU) dinoflagellate sequences from the same environmental samples, providing the largest, to date, set of dinoflagellate cob gene sequences and reliable estimates of total dinoflagellate richness within the samples and biogeographic comparisons between samples. This study also reports the presence of potentially toxic species of the genera Gambierdiscus, Ostreopsis, Coolia, Prorocentrum and Amphidinium from the above-mentioned geographical regions. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

Kohli, GS, Papiol, GG, Rhodes, LL, Harwood, DT, Selwood, A, Jerrett, A, Murray, SA & Neilan, BA 2014, 'A feeding study to probe the uptake of Maitotoxin by snapper (Pagrus auratus)', HARMFUL ALGAE, vol. 37, pp. 125-132.
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The role of ciguatoxins (CTX) in Ciguatera fish poisoning (CFP) has been investigated previously, but little is known about Maitotoxin (MTX) and whether it plays a significant role in causing human illness. The MTXs are known to have slightly higher potency than CTXs when administered intraperitoneally in mice, but are less potent when administered orally, due to their water solubility. It is not known whether MTXs accumulate in carnivorous fish tissues, and to investigate this further fish feeding trials with snapper (Pagrus auratus) were undertaken. Replicate P. auratus were fed with juvenile mullet (Aldrichetta forsteri) injected with a pellet of a known quantity of Gambierdiscus australes, which is a known producer of MTX. The levels of MTX in different fish tissues were determined using two newly developed sensitive LCMS/MS assays for MTX that monitor either a specific cleavage fragment (generated from micro-scale oxidation of the intact toxin) or the intact toxin itself. The investigations revealed the presence of MTX in P. auratus viscera, liver and muscle samples. The presence of Gambierdiscus-related genes in P. auratus digestive organs was confirmed using DNA amplification technology.

Kondaveeti, S, Chejara, DR & Siddhanta, AK 2014, 'Synthesis of self-assembly of agarose-fatty acid ester nanoparticles', Indian Journal of Chemistry - Section A Inorganic, Physical, Theoretical and Analytical Chemistry, vol. 53, no. 6, pp. 679-687.
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Microwave assisted facile synthesis of hydrophobically modified nano-sized particulate esters of agarose and stearic and palmitic acids (Ag-SA and Ag-PA), employing carbodiimide chemistry has been described. The hydrophobically modified agarose is capable of forming self-assembled nano-sized particles. Physicochemical characterization of Ag-SA, Ag-PA has been carried out by gel permeation chromatography, differential scanning calorimetric, scanning electron microscopy and FT-IR, 13C-NMR and 1H-NMR spectra. The aqueous self-assembly of the modified polymer has been studied by dynamic light scattering and transmission electron microscopy, which shows the formation of 4-5 nm micelles, and 220-250 nm polymeric vesicles. TEM images demonstrate that the self-aggregate is spherical in shape. These new agarose based nanosized materialsmay be of potential utility in biomedical applications as drug delivery vehicles.

Kondaveeti, S, Kumar, S, Ganesan, MS & Siddhanta, AK 2014, 'Galactans of Gracilaria pudumadamensis (Gracilariales, Rhodophyta) of Indian Waters', Natural Product Communications, vol. 9, no. 9, pp. 1934578X1400900-1934578X1400900.
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Galactans from the Indian agarophyte Gracilaria pudumadamensis were extracted and characterized. The isolated native (GPNative) and alkali treated (GPAlkali) galactans were characterized by IR, 13C NMR, GC-MS and GPC. It was found that GPNative and GPAlkali were composed mainly of 3,6-anhydro L-galactose, 6- O-methylated D-galactose and galactose in various mole proportions (15.6:69.9:17.5 mole% for GPNative and 20.2:69.8:10.0 mole% for GPAlkali). The GPNative and GPAlkali exhibited low gel strengths (<100 g/cm2) and high melting points (~76 °C), which may be due to the presence of high 6- O-Me-galactose contents. The latter, having low sulfate (2.1%), was by far the greatest 6- O-Me-galactose containing polysaccharide in a Gracilaria spp. reported in the literature. This methylated agar contained very low heavy metal ions estimated by inductively coupled plasma spectrophotometry (ICP). The results of this investigation would be useful in bioprospecting of agarophytes, especially those occurring in Indian waters and would be potentially useful in food, personal care and related domains.

Kondaveeti, S, Mehta, GK & Siddhanta, AK 2014, 'Modification of agarose: 6-Aminoagarose mediated syntheses of fluorogenic pyridine carboxylic acid amides', Carbohydrate Polymers, vol. 106, pp. 365-373.
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Kramarsky-Winter, E, Arotsker, L, Rasoulouniriana, D, Siboni, N, Loya, Y & Kushmaro, A 2014, 'The Possible Role of Cyanobacterial Filaments in Coral Black Band Disease Pathology', MICROBIAL ECOLOGY, vol. 67, no. 1, pp. 177-185.
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Black band disease (BBD), characterized by a black mat or line that migrates across a coral colony leaving behind it a bare skeleton, is a persistent disease affecting massive corals worldwide. Previous microscopic and molecular examination of this disease in faviid corals from the Gulf of Eilat revealed a number of possible pathogens with the most prominent being a cyanobacterium identified as Pseudoscillatoria coralii. We examined diseased coral colonies using histopathological and molecular methods in order to further assess the possible role of this cyanobacterium, its mode of entry, and pathological effects on the coral host tissues. Affected areas of colonies with BBD were sampled for examination using both light and transmission electron microscopies. Results showed that this dominant cyanobacterium was found on the coral surface, at the coral-skeletal interface, and invading the polyp tissues and gastrovascular cavity. Although tissues surrounding the invasive cyanobacterial filaments did not show gross morphological alterations, microscopic examination revealed that the coral cells surrounding the lesion were dissociated, necrotic, and highly vacuolated. No amoebocytes were evident in the mesoglea of affected tissues suggesting a possible repression of the coral immune response. Morphological and molecular similarity of the previously isolated BBD-associated cyanobacterium P. coralii to the current samples strengthens the premise that this species is involved in the disease in this coral. These results indicate that the cyanobacteria may play a pivotal role in this disease and that the mode of entry may be via ingestion, penetrating the coral via the gastrodermis, as well as through the skeletal-tissue interface.

Kula, A, Król, M, Wietecha-Posłuszny, R, Woźniakiewicz, M & Kościelniak, P 2014, 'Application of CE-MS to examination of black inkjet printing inks for forensic purposes', Talanta, vol. 128, no. 1, pp. 92-101.
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The dominant conception of forensic science as a patchwork of disciplines primarily assisting the criminal justice system (defined as 'forensics' in this article) is in crisis, or at least shows a series of anomalies and serious limitations. While the symptoms have been largely discussed previously, we argue that many of the commonly suggested solutions may not solve the fundamental problem. As a solution, we propose the forensic science community revive the forensic science perspective from its historical roots; that is, the study of crime and its traces. This will lead to the development of holistic models to provide a strategy to integrate technologies, and to help scientists develop their potential to engage in a more significant way in policing, crime investigation and, more generally, in criminology, instead of further compartmentalising the various forensic fields.

Kumar, M, Kumari, P, Reddy, CRK & Jha, B 2014, 'Salinity and Desiccation Induced Oxidative Stress Acclimation in Seaweeds', Advances in Botanical Research, vol. 71, pp. 91-123.
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Marine macroalgae, commonly known as seaweeds, are assemblage of diverse groups of phototrophic marine plants and form the base of the marine trophic pyramid. Rocky intertidal zones are the most dynamic and comprises of highly stressful habitats for marine life including seaweeds. They often experience severe environmental stress as a result of periodic exposure to a wide range of ambient conditions including intense radiation, high temperature, desiccation and salinity with turning tides. The relative abundance, survivability and distribution of seaweeds in such environments are principally determined by their tolerance abilities to diverse environmental stresses. Any adverse effect on seaweeds as a result of fluctuating environmental conditions can directly or indirectly lead to perturbations at higher trophic levels and eventually affect the integrity and sustainability of aquatic ecosystems. The recent proteome, transcriptome, metabolome and other biochemical analysis of seaweeds under oxidative stress have suggested the involvement of mannitol, proline, abscisic acid, polyamines, polyunsaturated fatty acids, oxylipins and fatty acid desaturases among others defending the seaweeds from diverse environmental stress. Both salinity and desiccation stresses are comparable in the context of a reduction of cellular water potential but differ in physiological process of ions uptake and their ratio determines the acclimation potential of seaweeds. In this chapter, we describe various tolerance and adaptive strategies of seaweeds in response to salinity fluctuations and desiccation induced oxidative stress at both biochemical and molecular levels enabling them to endure successfully for extended periods of stresses. Further, the new opportunities that became available from whole genome sequences of the brown alga Ectocarpus siliculosus and the red alga Chondrus crispus, in gaining newer insights into the cellular mechanisms of stress tolerance at molecular l...

Kumari, P, Kumar, M, Reddy, CRK & Jha, B 2014, 'Nitrate and Phosphate Regimes Induced Lipidomic and Biochemical Changes in the Intertidal Macroalga Ulva lactuca (Ulvophyceae, Chlorophyta)', Plant and Cell Physiology, vol. 55, no. 1, pp. 52-63.
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This study was carried out in order to understand the lipid and biochemical alterations resulting from different nutritional regimes of nitrate and phosphate in Ulva lactuca. The algal thalli cultured in artificial seawater (ASW) showed higher levels of carbohydrates and non-polar lipids and increased phosphatase activities, accompanied by degradation of polar lipids, proteins and pigments. Further, higher levels of lipid hydroperoxides indicated reative oxygen species (ROS)-mediated non-enzymatic lipid peroxidation due to nutritional limitation-induced oxidative stress. Those thalli cultured in ASW supplemented with nitrate showed responses corresponding to nitrate addition, such as an increase in pigments, monogalactosyldiacylglycerols, polyunsaturated fatty acids and nitrate reductase. In addition, these thalli showed partial induction of phosphatases, low phospholipids, and high sulfolipid and 1,2-diacylglyceryl-3-O-4′-(N,N,N-trimethyl)-homoserine (DGTS) due to phosphate limitation. Similarly, algal thalli cultured in ASW supplemented with phosphate showed down-regulation of phosphatases, an increase in phospholipids due to availability of phosphate as well as a decrease in nitrate reductase, pigment, monogalactosyldiacylglycerols and polyunsaturated fatty acids due to nitrate limitation. On the other hand, algal thalli cultured in ASW supplemented with both nitrate and phosphate showed recovery of lost pigments and proteins, a high monogalactosyldiacylglycerol/digalactosyldiacylglycerol ratio, high unsaturation and high oxylipin levels (both C18 and C20). Further, the accumulation of indole-3-acetic acid in nutrient-limited thalli and of kinetin and kinetin riboside in nutrient-supplemented thalli indicated their antagonistic roles under nutrient stress. Thus, U. lactuca copes with nitrate and phosphate nutritional stress by altering the metabolic pathways involved in lipid biosynthesis including a shift in lipid classes, fatty acids, oxylipins and...

Kunz, H-H, Gierth, M, Herdean, A, Satoh-Cruz, M, Kramer, DM, Spetea, C & Schroeder, JI 2014, 'Plastidial transporters KEA1, -2, and -3 are essential for chloroplast osmoregulation, integrity, and pH regulation in Arabidopsis', Proceedings of the National Academy of Sciences, vol. 111, no. 20, pp. 7480-7485.
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Significance Photosynthesis is the key biochemical reaction in plants. The molecular mechanisms of potassium (K + ) transport across chloroplast membranes and their relevance for chloroplast function and photosynthesis remain unknown. In our report, we identify and characterize the molecular basis of K + (KEA1, KEA2, KEA3) and sodium (NHD1) transporters in chloroplast membranes. We demonstrate that these inner envelope and thylakoid-targeted transporters are essential for chloroplast osmoregulation and thylakoid density. In addition, we discover an unexpected high Na + restoration of photosynthetic activity in the mutants.

Laczka, O, Labbate, M & Doblin, M 2014, 'Application of an ELISA-type amperometric assay to the detection of Vibrio species with screen-printed electrodes', ANALYTICAL METHODS, vol. 6, no. 7, pp. 2020-2023.
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Laczka, OF, Labbate, M, Seymour, JR, Bourne, DG, Fielder, SS & Doblin, MA 2014, 'Surface Immuno-Functionalisation for the Capture and Detection of Vibrio Species in the Marine Environment: A New Management Tool for Industrial Facilities', PLOS ONE, vol. 9, no. 10.
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Lai, S, Yang, Z, Liao, J, Li, J, Shao, B, Qiu, J & Song, Z 2014, 'Preparation and photoluminescence property of SiO 2 :Tb 3+ three dimensionally ordered macroporous composites including Ag nanoparticles', Journal of Non-Crystalline Solids, vol. 405, pp. 176-179.
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Lai, S, Yang, Z, Liao, J, Qiu, J, Song, Z, Yang, Y & Zhou, D 2014, 'Investigation of persistent luminescence property of Bi 3+, Dy 3+ co-doped CdSiO 3 phosphor', Materials Research Bulletin, vol. 60, pp. 714-718.
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Lapine, M, Shadrivov, IV & Kivshar, YS 2014, 'Colloquium: Nonlinear metamaterials', Reviews of Modern Physics, vol. 86, no. 3, pp. 1093-1123.
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© 2014 American Physical Society. This Colloquium presents an overview of the research on nonlinear electromagnetic metamaterials. The developed theoretical approaches and experimental designs are summarized, along with a systematic description of various phenomena available with nonlinear metamaterials.

Lauro, FM, Senstius, SJ, Cullen, J, Neches, R, Jensen, RM, Brown, MV, Darling, AE, Givskov, M, McDougald, D, Hoeke, R, Ostrowski, M, Philip, GK, Paulsen, IT & Grzymski, JJ 2014, 'The Common Oceanographer: Crowdsourcing the Collection of Oceanographic Data', PLOS BIOLOGY, vol. 12, no. 9, pp. e1001947-e1001947.
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Lavery, TJ, Roudnew, B, Seymour, J, Mitchell, JG, Smetacek, V & Nicol, S 2014, 'Whales sustain fisheries: Blue whales stimulate primary production in the Southern Ocean', Marine Mammal Science, vol. 30, no. 3, pp. 888-904.
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AbstractIt has previously been asserted that baleen whales compete with fisheries by consuming potentially harvestable marine resources. The regularly applied “surplus‐yield model” suggests that whale prey becomes available to fisheries if whales are removed, and has been presented as a justification for whaling. However, recent findings indicate that whales enhance ecosystem productivity by defecating iron that stimulates primary productivity in iron‐limited waters. While juvenile whales and whales that are pregnant or lactating retain iron for growth and milk production, nonbreeding adult whales defecate most of the iron they consume. Here, we modify the surplus‐yield model to incorporate iron defecation. After modeling a simplistic trajectory of blue whale recovery to historical abundances, the traditional surplus‐yield model predicts that 1011 kg of carbon yr−1 would become unavailable to fisheries. However, this ignores the nutrient recycling role of whales. Our model suggests the population of blue whales would defecate 3 × 106 kg of iron yr−1, which would stimulate primary production equivalent to that required to support prey consumption by the blue whale population. Thus, modifying the surplus‐yield model to include iron defecation indicates that blue whales do not render marine resources unavailable to fisheries. By defecating iron‐rich feces, blue whales promote Southern Ocean productivity, rather than reducing fishery yields.

Lawrence, A, K. Nicholls, S, H. Stansfield, S & M. Huston, W 2014, 'Characterization of the tail-specific protease (Tsp) from Legionella', The Journal of General and Applied Microbiology, vol. 60, no. 3, pp. 95-100.
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Bacterial tail-specific proteases (Tsps) have been attributed a wide variety of functions including intracellular virulence, cell wall morphology, proteolytic signal cascades and stress response. This study tested the hypothesis that Tsp has a key function for the transmissive form of Legionella pneumophila. A tsp mutant was generated in Legionella pneumophila 130b and the characteristics of this strain and the isogenic wild-type were examined using a range of growth and proteomic analyses. Recombinant Tsp protein was also produced and analyzed. The L. pneumophila tsp mutant showed no defect in growth on rich media or during thermo-osmotic stress conditions. In addition, no defects in cellular morphology were observed when the cells were examined using transmission electron microscopy. Purified recombinant Tsp was found to be an active protease with a narrow substrate range. Proteome analysis using iTRAQ (5% coverage of the proteome) found that, of those proteins detected, only 5 had different levels in the tsp mutant compared to the wild type. ACP (Acyl Carrier Protein), which has a key role for Legionella differentiation to the infectious form, was reduced in the tsp mutant; however, tsp- was able to infect and replicate inside macrophages to the same extent as the wild type. Combined, these data demonstrate that Tsp is a protease but is not essential for Legionella growth or cell infection. Thus, Tsp may have functional redundancy in Legionella. © 2014 Applied Microbiology, Molecular and Cellular Biosciences Research Foundation.

Le Brun, AP, Clifton, LA, Halbert, CE, Lin, B, Meron, M, Holden, PJ, Lakey, JH & Holt, SA 2014, 'Correction to Structural Characterization of a Model Gram-Negative Bacterial Surface Using Lipopolysaccharides from Rough Strains of Escherichia coli', Biomacromolecules, vol. 15, no. 8, pp. 3213-3213.
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Le, T-N, Schumann, U, Smith, NA, Tiwari, S, Au, PCK, Zhu, Q-H, Taylor, JM, Kazan, K, Llewellyn, DJ, Zhang, R, Dennis, ES & Wang, M-B 2014, 'DNA demethylases target promoter transposable elements to positively regulate stress responsive genes in Arabidopsis', GENOME BIOLOGY, vol. 15, no. 9, pp. 1-18.
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BACKGROUND: DNA demethylases regulate DNA methylation levels in eukaryotes. Arabidopsis encodes four DNA demethylases, DEMETER (DME), REPRESSOR OF SILENCING 1 (ROS1), DEMETER-LIKE 2 (DML2), and DML3. While DME is involved in maternal specific gene expression during seed development, the biological function of the remaining DNA demethylases remains unclear. RESULTS: We show that ROS1, DML2, and DML3 play a role in fungal disease resistance in Arabidopsis. A triple DNA demethylase mutant, rdd (ros1 dml2 dml3), shows increased susceptibility to the fungal pathogen Fusarium oxysporum. We identify 348 genes differentially expressed in rdd relative to wild type, and a significant proportion of these genes are downregulated in rdd and have functions in stress response, suggesting that DNA demethylases maintain or positively regulate the expression of stress response genes required for F. oxysporum resistance. The rdd-downregulated stress response genes are enriched for short transposable element sequences in their promoters. Many of these transposable elements and their surrounding sequences show localized DNA methylation changes in rdd, and a general reduction in CHH methylation, suggesting that RNA-directed DNA methylation (RdDM), responsible for CHH methylation, may participate in DNA demethylase-mediated regulation of stress response genes. Many of the rdd-downregulated stress response genes are downregulated in the RdDM mutants nrpd1 and nrpe1, and the RdDM mutants nrpe1 and ago4 show enhanced susceptibility to F. oxysporum infection. CONCLUSIONS: Our results suggest that a primary function of DNA demethylases in plants is to regulate the expression of stress response genes by targeting promoter transposable element sequences.

Lee, JC, Bracher, DO, Cui, S, Ohno, K, McLellan, CA, Zhang, X, Andrich, P, Aleman, B, Russell, KJ, Magyar, AP, Aharonovich, I, Jayich, AB, Awschalom, D & Hu, EL 2014, 'Deterministic coupling of delta-doped NV centers to a nanobeam photonic crystal cavity', Applied Physics Letters, vol. 105, no. 26.
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The negatively-charged nitrogen vacancy center (NV) in diamond has generatedsignificant interest as a platform for quantum information processing andsensing in the solid state. For most applications, high quality opticalcavities are required to enhance the NV zero-phonon line (ZPL) emission. Anoutstanding challenge in maximizing the degree of NV-cavity coupling is thedeterministic placement of NVs within the cavity. Here, we report photoniccrystal nanobeam cavities coupled to NVs incorporated by a delta-dopingtechnique that allows nanometer-scale vertical positioning of the emitters. Wedemonstrate cavities with Q up to ~24,000 and mode volume V ~$0.47({\lambda}/n)^{3}$ as well as resonant enhancement of the ZPL of an NVensemble with Purcell factor of ~20. Our fabrication technique provides a firststep towards deterministic NV-cavity coupling using spatial control of theemitters.

Lee, KWK, Periasamy, S, Mukherjee, M, Xie, C, Kjelleberg, S & Rice, SA 2014, 'Biofilm development and enhanced stress resistance of a model, mixed-species community biofilm', The ISME Journal, vol. 8, no. 4, pp. 894-907.
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Abstract Most studies of biofilm biology have taken a reductionist approach, where single-species biofilms have been extensively investigated. However, biofilms in nature mostly comprise multiple species, where interspecies interactions can shape the development, structure and function of these communities differently from biofilm populations. Hence, a reproducible mixed-species biofilm comprising Pseudomonas aeruginosa, Pseudomonas protegens and Klebsiella pneumoniae was adapted to study how interspecies interactions affect biofilm development, structure and stress responses. Each species was fluorescently tagged to determine its abundance and spatial localization within the biofilm. The mixed-species biofilm exhibited distinct structures that were not observed in comparable single-species biofilms. In addition, development of the mixed-species biofilm was delayed 1–2 days compared with the single-species biofilms. Composition and spatial organization of the mixed-species biofilm also changed along the flow cell channel, where nutrient conditions and growth rate of each species could have a part in community assembly. Intriguingly, the mixed-species biofilm was more resistant to the antimicrobials sodium dodecyl sulfate and tobramycin than the single-species biofilms. Crucially, such community level resilience was found to be a protection offered by the resistant species to the whole community rather than selection for the resistant species. In contrast, community-level resilience was not observed for mixed-species planktonic cultures. These findings suggest that community-level interactions, such as sharing of public goods, are unique to the structured biofilm community, where the members are closely associated with each other.

Leggio, GM, Camillieri, G, Platania, CBM, Castorina, A, Marrazzo, G, Torrisi, SA, Nona, CN, D'Agata, V, Nobrega, J, Stark, H, Bucolo, C, Le Foll, B, Drago, F & Salomone, S 2014, 'Dopamine D3 Receptor Is Necessary for Ethanol Consumption: An Approach with Buspirone', Neuropsychopharmacology, vol. 39, no. 8, pp. 2017-2028.
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Leigh, A, Hill, R & Ball, MC 2014, 'Leaf shape influences spatial variation in photosynthetic function in Lomatia tinctoria', Functional Plant Biology, vol. 41, no. 8, pp. 833-833.
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A relationship exists between the two-dimensional shape of leaves and their venation architecture, such that broad or broad-lobed leaves can have leaf tissue far from major veins, potentially creating stronger gradients in water potential – and associated photosynthetic function – than found across narrow counterparts. We examined the spatial patterns of photosynthetic efficiency (ΔF/Fm′) and non-photochemical quenching (NPQ) in response to increased vapour pressure deficit (VPD) using two morphs of Lomatia tinctoria (Labill.) R.Br: those with broad-lobed and those with narrow-lobed leaves. Stomatal conductance (gs), instantaneous water use efficiency (WUE), stomatal and minor veins density also were measured. ΔF/Fm′ decreased with stress but was higher and less spatially heterogeneous across broad than narrow lobes. The strongest depression in ΔF/Fm′ in broad lobes was at the edges and in narrow lobes, the tips. Non-photochemical quenching was spatially more varied in broad lobes, increasing at the edges and tips. Variation in photosynthetic function could not be explained by gs, WUE or minor vein density, whereas proximity to major veins appeared to mitigate water stress at the tips only for broad lobes. Our findings indicate that the relationship between venation architecture and water delivery alone can partially explain the spatial pattern of photosynthetic function.

Lem, LLC, Phillips, MR & Ton-That, C 2014, 'Controlling the visible luminescence in hydrothermal ZnO', JOURNAL OF LUMINESCENCE, vol. 154, pp. 387-391.
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Cathodoluminescence spectra have been measured in hydrothermal and hydrogen-doped ZnO at different excitation densities and temperatures to investigate the emission efficiencies of near-band-edge (NBE), green and yellow luminescence bands. The NBE intensity depends linearly on the electron beam excitation as expected for excitonic recombination character. The intensities of the green and yellow bands are highly dependent not only on the excitation density but also on temperature. At high excitation densities ZnO exhibits dominant green emission at room temperature; the intensity of the green band can be further controlled by doping ZnO with hydrogen, which passivates green luminescence centers. Conversely at small excitation densities (< 0.1 nA) and low temperatures the visible luminescence from ZnO is predominantly yellow due to the abundance of Li in hydrothermal ZnO. The results are explained by differences in the recombination kinetics and the relative concentrations of the green and yellow centers, and illustrate that single-color emission can be achieved in ZnO by adjusting the excitation power and temperature. © 2014 Published by Elsevier B.V. All rights reserved.

Letnic, M, Webb, JK, Jessop, TS, Florance, D & Dempster, T 2014, 'Artificial water points facilitate the spread of an invasive vertebrate in arid Australia', JOURNAL OF APPLIED ECOLOGY, vol. 51, no. 3, pp. 795-803.
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Summary: The spread of invasive species after their initial introduction is often facilitated by human actions. In some cases, invaders only become established in habitats where dominant native species have been displaced as a result of human actions or where humans inadvertently provide essential resources such as food, water or shelter. We investigated if dams that provide water for livestock have facilitated the cane toad's (Rhinella marina) invasion of a hot semi-arid landscape by providing toads with a resource subsidy and hence refuge from extreme heat and aridity. To determine the relationship between the presence of surface water and habitat occupancy by toads, we surveyed natural and artificial water features for cane toads during the annual dry season. We used radiotracking and acoustic tags to determine whether movement patterns and shelter use of cane toads were focussed around dams. To determine whether dams provide toads with refuge from extreme heat and aridity, we deployed plaster models with internal thermometers to estimate ambient temperatures and toad desiccation rates in shelter sites. To determine whether dams alleviate the stress experienced by toads, we measured plasma corticosterone levels of toads that sheltered in and away from dams. Toads were present in sites with standing water and absent from waterless sites. Most radiotracked toads sheltered within 1 m of water. Toad movements were focussed around water. Toads tracked with passive acoustic telemetry over a 6-month dry season were highly resident at dams. Plaster models placed in toad shelter sites away from the water lost 27% more mass and experienced higher temperatures than models placed near the water's edge. Toads that sheltered in terrestrial shelters exhibited higher plasma corticosterone levels compared to toads that sheltered near dams. Dams provide toads with refuge habitats where they are less at risk from overheating and dehydration. Synthesis and applications....

Li, F, Harry, EJ, Bottomley, AL, Edstein, MD, Birrell, GW, Woodward, CE, Keene, FR & Collins, JG 2014, 'Dinuclear ruthenium(II) antimicrobial agents that selectively target polysomes in vivo', CHEMICAL SCIENCE, vol. 5, no. 2, pp. 685-693.
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Wide-field fluorescence microscopy at high magnification was used to study the intracellular binding site of Rubb16 in Escherichia coli. Upon incubation of E. coli cells at the minimum inhibitory concentration, Rubb 16 localised at ribosomes with no significant DNA binding observed. Furthermore, Rubb16 condensed the ribosomes when they existed as polysomes. It is postulated that the condensation of polysomes would halt protein production, and thereby inhibit bacterial growth. The results of this study indicate that the family of inert dinuclear ruthenium complexes Rubb n selectively target RNA over DNA in vivo. Selective RNA targeting could be advantageous for the development of therapeutic agents, and because of differences in ribosome structure between bacteria and eukaryotic cells, the Rubbn complexes could be selectively toxic to bacteria. In support of this hypothesis, the toxicity of Rubb16 was found to be significantly less to liver and kidney cell lines than against a range of bacteria. © 2014 The Royal Society of Chemistry.

Li, H, Staudenmayer, J & Carroll, RJ 2014, 'Hierarchical functional data with mixed continuous and binary measurements', Biometrics, vol. 70, no. 4, pp. 802-811.
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SummaryMotivated by objective measurements of physical activity, we take a functional data approach to longitudinal data with simultaneous measurement of a continuous and a binary outcomes. The regression structures are specified as smooth curves measured at various time‐points with random effects that have a hierarchical correlation structure. The random effect curves for each variable are summarized using a few important principal components, and the association of the two longitudinal variables is modeled through the association of the principal component scores. We use penalized splines to model the mean curves and the principal component curves, and cast the proposed model into a mixed effects model framework for model fitting, prediction and inference. Via a quasilikelihood type approximation for the binary component, we develop an algorithm to fit the model. Data‐based transformation of the continuous variable and selection of the number of principal components are incorporated into the algorithm. The method is applied to the motivating physical activity data and is evaluated empirically by a simulation study. Extensions for different types of outcomes are also discussed.

Li, K, Liu, H & Wang, G 2014, 'Sb2O3 Nanowires as Anode Material for Sodium-Ion Battery', ARABIAN JOURNAL FOR SCIENCE AND ENGINEERING, vol. 39, no. 9, pp. 6589-6593.
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The anodic properties of antimony trioxide (Sb2O3) nanowires were investigated as electrode material for sodium-ion battery. Sb2O3 nanowires were prepared via a mild-condition, solvothermal route based on the hydrolysis of antimony trichloride (SbCl3) in alcohol aqueous solution. The uniform morphology and crystal phases of Sb2O3 nanowires are confirmed by scanning electronic microscopy, transmission electronic microscopy, and X-ray diffraction. The electrochemical performance of Sb2O3 nanowire anodes was studied and thematerial exhibits a high reversible capacity of 230 mAh/g which is attributed to the reversible complex conversion-alloying reactions between antimony trioxide and sodium.

Li, K, Wang, S, Wen, S, Tang, Y, Li, J, Shi, X & Zhao, Q 2014, 'Enhanced In Vivo Antitumor Efficacy of Doxorubicin Encapsulated within Laponite Nanodisks', ACS Applied Materials & Interfaces, vol. 6, no. 15, pp. 12328-12334.
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Li, RQ, Qiu, JB, Yang, ZW, Liao, JY, Wu, HJ, Lai, SF, Song, ZG, Yang, Y, Zhou, DC & Wang, RF 2014, 'Preparation and up-conversion luminescence properties of Yb³⁺/Tm³⁺ Co-doped Sb2O4 powder', Guang Pu Xue Yu Guang Pu Fen Xi/Spectroscopy and Spectral Analysis, vol. 34, no. 3, pp. 630-633.
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The Sb2O4:Yb3+, Tm3+ up-conversion luminescence powder with excellent physical, chemical stability and relative low phonon energy was synthesized by the high temperature solid-state reaction and its up-conversion luminescence property was investigated. Under the 980 nm excitation, infrared and blue up-conversion emissions centered at 800 and 480 nm were observed, which were assigned to the 1G4→3H6 and 3H4→3H6 transitions of Tm3+, respectively. The influence of Yb3+ and Tm3+ concentration on the up-conversion emission property was also obtained. The up-conversion luminescence increases with increasing of Yb3+ and Tm3+ concentration. Additionally, the up-conversion luminescence mechanism was discussed based on the dependence of Tm3+ up-conversion luminescence on pump power. It is interesting that two photon excitation processes for blue and infrared emission were observed in the Sb2O4:Yb3+, Tm3+ powder under a 980 nm excitation. Based on the energy level diagram of Tm3+ and Yb3+ ions, we think that two photons blue emission is contributed to the cooperation energy transfer between Tm3+ and Yb3+ ions. We believe that the Sb2O4:Yb3+, Tm3+ up-conversion luminescence powder will have potential application for new optical devices in up-conversion color displays, sensors, detection of infrared radiation, and lasers.

Li, R-Q, Qiu, J-B, Yang, Z-W, Liao, J-Y, Wu, H-J, Lai, S-F, Song, Z-G, Yang, Y, Zhou, D-C & Wang, R-F 2014, '[Preparation and up-conversion luminescence properties of Yb3+/Tm3+ co-doped Sb2O4 powder].', Guang Pu Xue Yu Guang Pu Fen Xi, vol. 34, no. 3, pp. 630-633.
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The Sb2O4:Yb3+, Tm3+ up-conversion luminescence powder with excellent physical, chemical stability and relative low phonon energy was synthesized by the high temperature solid-state reaction and its up-conversion luminescence property was investigated. Under the 980 nm excitation, infrared and blue up-conversion emissions centered at 800 and 480 nm were observed, which were assigned to the 1G4-->3H6 and 3H4-->3 He transitions of Tm2+, respectively. The influence of Yb3+ and Tm3+ concentration on the up-conversion emission property was also obtained. The up-conversion luminescence increases with increasing of Yb3+ and Tm3+ concentration. Additionally, the up-conversion luminescence mechanism was discussed based on the dependence of Tm3+ up-conversion luminescence on pump power. It is interesting that two photon excitation processes for blue and infrared emission were observed in the Sb2O04: Yb3+, Tm3+ powder under a 980 nm excitation. Based on the energy level diagram of Tma3 and Yb2+ ions, we think that two photons blue emission is contributed to the cooperation energy transfer between Tm'+ and Yb3+ ions. We believe that the Sbz04 : Yb3 , Tm2+ up-conversion luminescence powder will have potential application for new optical devices in up-conversion color displays, sensors, detection of infrared radiation, and lasers.

Liao, J, Yang, Z, Lai, S, Shao, B, Li, J, Qiu, J, Song, Z & Yang, Y 2014, 'Upconversion Emission Enhancement of NaYF₄:Yb,Er Nanoparticles by Coupling Silver Nanoparticle Plasmons and Photonic Crystal Effects', The Journal of Physical Chemistry C, vol. 118, no. 31, pp. 17992-17999.
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Metal nanoparticle plasmons or the photonic crystal effect are being widely used to modify luminescence properties of materials. However, coupling of surface plasmons with photonic crystals are seldom reported for enhancing luminescence of materials. In this paper, a new method for upconversion emission enhancement of rare-earth doped nanoparticles is reported, attributed to the coupling of surface plasmons with photonic band gap effects. Opal/Ag hybrid substrates were prepared by depositing Ag nanoparticles on the top layer of opals by magnetron sputtering. The selective enhancement of red or green upconversion emission of NaYF4:Yb3+,Er3+ nanoparticles on the opal/Ag hybrid substrates is attributed to the coupling effect of surface plasmons and Bragg reflection of the photonic band gap. In addition, the upconversion emission enhancement of NaYF4:Yb 3+,Er3+ nanoparticles on the opal/Ag hybrid substrate is attributed to the excitation enhancement was obtained when the excitation light wavelengths overlap with the photonic band gaps of opal/Ag hybrid substrates. We believe that these enhancement effects based on the coupling of metal nanoparticles with the photonic band gap could be extended to other light-emitting materials, which may result in a new generation of lighting devices. © 2014 American Chemical Society.

Liao, J, Yang, Z, Wu, H, Lai, S, Qiu, J, Song, Z, Yang, Y & Yin, Z 2014, 'Continuous modification of upconversion luminescence of fluorescent dye in the crystalline colloidal arrays', Colloid and Polymer Science, vol. 292, no. 3, pp. 613-617.
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The crystalline colloidal arrays with controllable photonic bandgaps were prepared by the change of volume fraction of the polystyrene microspheres. Upconversion emission property of fluorescent dye has investigated in crystalline colloidal array, and continuous modification of the upconversion emission of fluorescent dye was observed. A significant suppression of upconversion emission of dye in the range of the photonic bandgap as well as enhancement at the bandgap edge was obtained in the crystalline colloidal arrays. In addition, upconversion emission of dye was also enhanced when the excited light overlapped with the long or short bandgap edge of the crystalline colloidal arrays, which is due to slow photons effect near the edges of a photonic bandgap. The continuous modification and enhancement of upconversion emission may be important for the development of low-threshold upconversion lasers and displays. © 2013 Springer-Verlag.

LIAO, J, YANG, Z, WU, H, LAI, S, QIU, J, SONG, Z, YANG, Y, ZHOU, D & YIN, Z 2014, 'UPCONVERSION LUMINESCENCE ENHANCEMENT OF NaYF₄:Yb³⁺, Er³⁺ NANOPARTICLES ON INVERSE OPAL SURFACE', Surface Review and Letters, vol. 21, no. 01, pp. 1450017-1450017.
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LaPO 4 inverse opal photonic crystals with different photonic band gaps were fabricated by template-assisted method. The Yb 3+/ Er 3+ co-doped NaYF 4 nanoparticles were deposited on the surfaces of the inverse opals, and their up-conversion emission properties were investigated. The upconversion emissions of Yb 3+/ Er 3+ co-doped NaYF 4 nanoparticles on the inverse opal surfaces have been enhanced when the upconversion emission bands of the nanoparticles are in the range of photonic band gaps of the inverse opals, which is attributed to an efficient and selective reflection of photonic band gaps.

Lim, CED & Cheng, NCL 2014, 'What do we know about needling sensation (de qi) and Bell's palsy outcome?', Focus on Alternative and Complementary Therapies, vol. 19, no. 1, pp. 34-35.
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Lim, CED, Cheng, NCL & Lengacher, CA 2014, 'Effect of mindfulness based stress reduction in stage 0‐III breast cancer survivors', Focus on Alternative and Complementary Therapies, vol. 19, no. 4, pp. 219-220.
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Limbri, H, Gunawan, C, Thomas, T, Smith, A, Scott, J & Rosche, B 2014, 'Coal-Packed Methane Biofilter for Mitigation of Green House Gas Emissions from Coal Mine Ventilation Air', PLoS ONE, vol. 9, no. 4, pp. e94641-e94641.
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Methane emitted by coal mine ventilation air (MVA) is a significant greenhouse gas. A mitigation strategy is the oxidation of methane to carbon dioxide, which is approximately twenty-one times less effective at global warming than methane on a mass-basis. The low non-combustible methane concentrations at high MVA flow rates call for a catalytic strategy of oxidation. A laboratory-scale coal-packed biofilter was designed and partially removed methane from humidified air at flow rates between 0.2 and 2.4 L min -1 at 30°C with nutrient solution added every three days. Methane oxidation was catalysed by a complex community of naturally-occurring microorganisms, with the most abundant member being identified by 16S rRNA gene sequence as belonging to the methanotrophic genus Methylocystis. Additional inoculation with a laboratorygrown culture of Methylosinus sporium, as investigated in a parallel run, only enhanced methane consumption during the initial 12 weeks. The greatest level of methane removal of 27.260.66 g methane m23 empty bed h21 was attained for the non-inoculated system, which was equivalent to removing 19.762.9% methane from an inlet concentration of 1% v/v at an inlet gas flow rate of 1.6 L min21 (2.4 min empty bed residence time). These results show that low-cost coal packing holds promising potential as a suitable growth surface and contains methanotrophic microorganisms for the catalytic oxidative removal of methane.©2014 Limbri et al.

Lin, G, Makarov, D, Melzer, M, Si, W, Yan, C & Schmidt, OG 2014, 'A highly flexible and compact magnetoresistive analytic device', Lab Chip, vol. 14, no. 20, pp. 4050-4058.
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A highly flexible GMR-based microfluidic analytic device was demonstrated to analyze droplets of various dimensions and different concentrations of magnetic contents.

Ling, GC, Low, MH, Erken, M, Longford, S, Nielsen, S, Poole, AJ, Steinberg, P, McDougald, D & Kjelleberg, S 2014, 'Micro-fabricated polydimethyl siloxane (PDMS) surfaces regulate the development of marine microbial biofilm communities', Biofouling, vol. 30, no. 3, pp. 323-335.
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This study explored an antifouling (AF) concept based on deployment of microfabricated polydimethyl siloxane (PDMS) surfaces with 1-10 μm periodicity corrugated topographies in temperate marine waters. The effect of the surfaces on the development of microbial biofilms over 28 days and during different seasons, including both summer and winter, was examined using confocal laser scanning microscopy (CLSM) as well as terminal restriction fragment (T-RF) analysis for phylogenetic fingerprinting. The microscale topography significantly impacted biofilm development by altering the attachment pattern and reducing microcolony formation on the 1, 2 and 4 μm PDMS surfaces. Also, field deployments over 28 days showed a significant reduction in biovolume on the 4 and 10 μm PDMS surfaces despite altered environmental conditions. The microfabricated PDMS surfaces further significantly impacted on the community composition of the biofilms, as revealed by changes in T-RF profiles, at different stages of development. Moreover, altered biofilm resistance was demonstrated by exposing pre-established biofilms on 10 μm micro-fabricated surfaces to enhanced flagellate predation by a heterotrophic protist, Rhynchomonas nasuta. Pronounced changes in the overall marine microbial biofilm development as well as community composition warrant exploring substratum modification for marine AF applications.

Little, MP, Kukush, AG, Masiuk, SV, Shklyar, S, Carroll, RJ, Lubin, JH, Kwon, D, Brenner, AV, Tronko, MD, Mabuchi, K, Bogdanova, TI, Hatch, M, Zablotska, LB, Tereshchenko, VP, Ostroumova, E, Bouville, AC, Drozdovitch, V, Chepurny, MI, Kovgan, LN, Simon, SL, Shpak, VM & Likhtarev, IA 2014, 'Impact of Uncertainties in Exposure Assessment on Estimates of Thyroid Cancer Risk among Ukrainian Children and Adolescents Exposed from the Chernobyl Accident', PLoS ONE, vol. 9, no. 1, pp. e85723-e85723.
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The 1986 accident at the Chernobyl nuclear power plant remains the most serious nuclear accident in history, and excess thyroid cancers, particularly among those exposed to releases of iodine-131 remain the best-documented sequelae. Failure to take dose-measurement error into account can lead to bias in assessments of dose-response slope. Although risks in the Ukrainian-US thyroid screening study have been previously evaluated, errors in dose assessments have not been addressed hitherto. Dose-response patterns were examined in a thyroid screening prevalence cohort of 13,127 persons aged <18 at the time of the accident who were resident in the most radioactively contaminated regions of Ukraine. We extended earlier analyses in this cohort by adjusting for dose error in the recently developed TD-10 dosimetry. Three methods of statistical correction, via two types of regression calibration, and Monte Carlo maximum-likelihood, were applied to the doses that can be derived from the ratio of thyroid activity to thyroid mass. The two components that make up this ratio have different types of error, Berkson error for thyroid mass and classical error for thyroid activity. The first regression-calibration method yielded estimates of excess odds ratio of 5.78 Gy-1 (95% CI 1.92, 27.04), about 7% higher than estimates unadjusted for dose error. The second regression-calibration method gave an excess odds ratio of 4.78 Gy-1 (95% CI 1.64, 19.69), about 11% lower than unadjusted analysis. The Monte Carlo maximum-likelihood method produced an excess odds ratio of 4.93 Gy-1 (95% CI 1.67, 19.90), about 8% lower than unadjusted analysis. There are borderline-significant (p= 0.101-0.112) indications of downward curvature in the dose response, allowing for which nearly doubled the low-dose linear coefficient. In conclusion, dose-error adjustment has comparatively modest effects on regression parameters, a consequence of the relatively small errors, of a mixture of Berkson and...

Liu, H, Wang, H, Xu, Y, Guo, R, Wen, S, Huang, Y, Liu, W, Shen, M, Zhao, J, Zhang, G & Shi, X 2014, 'Lactobionic Acid-Modified Dendrimer-Entrapped Gold Nanoparticles for Targeted Computed Tomography Imaging of Human Hepatocellular Carcinoma', ACS Applied Materials & Interfaces, vol. 6, no. 9, pp. 6944-6953.
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Liu, J, Liu, H, Yang, T, Wang, G & Tade, MO 2014, 'Mesoporous carbon with large pores as anode for Na-ion batteries', CHINESE SCIENCE BULLETIN, vol. 59, no. 18, pp. 2186-2190.
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Sodium ion (Na+) batteries have attracted increased attention for energy storage owing to the natural abundance and low cost of sodium. Herein, we report the synthesis of mesoporous carbon with large pores as anode for Na-ion batteries. The mesoporous carbon was obtained by carbonization and dense packing of 50 nm resorcinol and formaldehyde spheres synthesized through an extension Stöber method. Our work demonstrates that replacement of lithium by sodium using large pore carbon as anode might offer an alternative route for rechargeable batteries.

Liu, M, Powell, D, Shadrivov, I, Kivshar, Y & Lapine, M 2014, 'Chiral torsional metamaterials', Optics and Photonics News, vol. 25, no. 12, p. 51.

Liu, M, Powell, DA, Shadrivov, IV, Lapine, M & Kivshar, YS 2014, 'Spontaneous chiral symmetry breaking in metamaterials', Nature Communications, vol. 5, no. 1.
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Spontaneous chiral symmetry breaking underpins a variety of areas such as subatomic physics and biochemistry, and leads to an impressive range of fundamental phenomena. Here we show that this prominent effect is now available in artificial electromagnetic systems, enabled by the advent of magnetoelastic metamaterials where a mechanical degree of freedom leads to a rich variety of strong nonlinear effects such as bistability and self-oscillations. We report spontaneous symmetry breaking in torsional chiral magnetoelastic structures where two or more meta-molecules with opposite handedness are electromagnetically coupled, modifying the system stability. Importantly, we show that chiral symmetry breaking can be found in the stationary response of the system, and the effect is successfully demonstrated in a microwave pump-probe experiment. Such symmetry breaking can lead to a giant nonlinear polarization change, energy localization and mode splitting, which provides a new possibility for creating an artificial phase transition in metamaterials, analogous to that in ferrimagnetic domains. © 2014 Macmillan Publishers Limited.

Liu, Q, Yang, Y, Sun, B, Su, D, Li, Z, Xia, Q & Wang, G 2014, 'Hydrothermal synthesis of FeP4 and Fe2P-loaded alpha-Fe2O3 hollow spheres and applications in gas sensors', SENSORS AND ACTUATORS B-CHEMICAL, vol. 194, pp. 27-32.
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FeP4 and Fe2P-loaded hematite (α-Fe 2O3) (FFH) hollow spheres with a diameter of 130-410 nm were synthesized by a hydrothermal method. The structure and morphology of the FFH hollow spheres were characterized by X-ray diffraction (XRD), transmission electron microscope (TEM), field-emission scanning electron microscope (FESEM), and X-ray photoelectron spectroscopy (XPS). Nitrogen adsorption-desorption isothermal measurements revealed that the FFH hollow spheres have larger BET surface area and mesopores. The gas-sensing performance of the FFH hollow spheres was investigated towards a series of typical organic solvents and fuels. The FFH hollow spheres exhibited a superior sensitivity towards flammable and irritant gases. The possible sensing mechanism of the FFH hollow spheres sensor is also proposed. © 2013 Elsevier B.V.

Liu, S, Killen, E, Lim, M, Gunawan, C & Amal, R 2014, 'The effect of common bacterial growth media on zinc oxide thin films: identification of reaction products and implications for the toxicology of ZnO', RSC Adv., vol. 4, no. 9, pp. 4363-4370.
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This study provides a thorough investigation on the effects of the commonly-employed microbial growth medium, namely the peptide-containing luria-bertani broth, tryptic soy broth, the glucose-containing M9 Minimal Salts Media as well as phosphate-buffered saline solution on the dissolution and microstructural transformation of zinc oxide thin film. Morphology and chemical composition of the ZnO film after incubation in the media was thoroughly characterised. In addition, the amount and rate of soluble zinc released by the ZnO thin films was quantified. Exposure of ZnO thin film in the different growth media saw formation of new zinc compounds, resulting from various chemical reactions of zinc with the medium components. Deposition of the new zinc compounds on top of the thin film caused morphological transformation of the film. Zinc leaching was observed in all of the tested media, with significantly higher extent of dissolution observed in peptide-containing organic media, such as luria bertani and tryptic soy broth. Complex organic components, such as amino acids and peptides form complexes with zinc oxide coatings, resulting in complexation-mediated leaching of zinc. Soluble zinc re-precipitates with components in the media, and therefore substantially reduced the amount of dissolved zinc. The results suggest strong influence of solution chemistry on ZnO speciation in a test medium, which have important implications for the mechanistic interpretation of ZnO toxicity. © 2014 The Royal Society of Chemistry.

Liu, W, Wen, S, Jiang, L, An, X, Zhang, M, Wang, H, Zhang, Z, Zhang, G & Shi, X 2014, 'PLGA Hollow Microbubbles Loaded with Iron Oxide Nanoparticles and Doxorubicin for Dual-mode US/MR Imaging and Drug Delivery', Current Nanoscience, vol. 10, no. 4, pp. 543-552.
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Liu, W, Wen, S, Shen, M & Shi, X 2014, 'Doxorubicin-loaded poly(lactic-co-glycolic acid) hollow microcapsules for targeted drug delivery to cancer cells', New J. Chem., vol. 38, no. 8, pp. 3917-3924.
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Poly(lactic-co-glycolic acid) hollow microcapsules loaded with doxorubicin can be assembled with folate-functionalized polyethyleneimine for targeted drug delivery to cancer cells.

Lloyd, A, Russell, M, Blanes, L, Somerville, R, Doble, P & Roux, C 2014, 'The application of portable microchip electrophoresis for the screening and comparative analysis of synthetic cathinone seizures', Forensic Science International, vol. 242, pp. 16-23.
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Variation in the chemical composition of illicit tablets and powders is common among samples within a given drug seizure. Using microchip electrophoresis (ME), multiple tablets can be screened in a cost-effective and timely manner. This method could be used in conjunction with reporting methods that focus solely on statistical sampling to infer homogeneity or otherwise of a larger subset of tablets. Some frequently observed synthetic cathinones, often present in illicit tablets seized in New Zealand, were chosen for analysis. An ME device (Agilent Bioanalyzer 2100) was used to electrophoretically separate synthetic cathinones. The background electrolyte was composed of a 50. mM sodium tetraborate buffer with 50. mM sodium dodecyl sulphate at pH 9.66. Analytes were derivatised prior to analysis for 3. min at 90. °C, employing fluorescein isothiocyanate isomer I (FITC). A characteristic fluorescent profile was obtained for each tablet, in terms of the number of constituents, relative peak height ratios and migration times. The repeatability of the developed method was assessed for a wide range of tablets and relative standard deviations of 0.4-5.2% and 1.6-5.5% were calculated for migration times and peak height ratios, respectively. The use of microchip tablet profiles in the forensic case comparison of illicit drug seizure samples in realistic scenarios is discussed. © 2014 Elsevier Ireland Ltd.

Lockhart, PJ, Larkum, AWD, Becker, M & Penny, D 2014, 'We are Still Learning About the Nature of Species and Their Evolutionary Relationships¹', Annals of the Missouri Botanical Garden, vol. 100, no. 1-2, pp. 6-13.
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Loo, C-Y, Young, PM, Cavaliere, R, Whitchurch, CB, Lee, W-H & Rohanizadeh, R 2014, 'Silver nanoparticles enhance Pseudomonas aeruginosa PAO1 biofilm detachment', DRUG DEVELOPMENT AND INDUSTRIAL PHARMACY, vol. 40, no. 6, pp. 719-729.
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Loo, C-Y, Young, PM, Lee, W-H, Cavaliere, R, Whitchurch, CB & Rohanizadeh, R 2014, 'Non-cytotoxic silver nanoparticle-polyvinyl alcohol hydrogels with anti-biofilm activity: designed as coatings for endotracheal tube materials', BIOFOULING, vol. 30, no. 7, pp. 773-788.
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Endotracheal intubation is commonly associated with hospital-acquired infections as the intubation device acts as reservoir for bacterial colonization in the lungs. To reduce the incidence of bacterial colonization on the tubes, hydrogel coatings loaded with antimicrobial agents are gaining popularity. The aim of this study was to incorporate silver nanoparticles (AgNPs) into polyvinyl alcohol (PVA) to form stable hydrogels. Embedding AgNPs into PVA resulted in a decreased elongation at break and an increased tensile strength compared to PVA alone. The Ag release profile varied as a function of the degree of hydrolysis of PVA: the higher degree of hydrolysis demonstrated a lower release rate. Fourier infrared transform spectroscopy demonstrated that AgNPs interacted exclusively with the -OH groups of PVA. AgNP-loaded PVA was non-toxic against human normal bronchial epithelial cells while effective against the attachment of Pseudomonas aeruginosa and Staphylococcus aureus with a greater effect on P. aeruginosa. © 2014 © 2014 Taylor & Francis.

Loo, C-Y, Young, PM, Lee, W-H, Traini, D, Cavaliere, R, Whitchurch, CB & Rohanizadeh, R 2014, 'COMBINATION THERAPY OF CURCUMIN AND SILVER NANOPARTICLES WITH ENHANCED ANTI-BIOFILM ACTIVITY FOR TREATMENT OF ENDOTRACHEAL TUBE-ASSOCIATED INFECTIONS', JOURNAL OF AEROSOL MEDICINE AND PULMONARY DRUG DELIVERY, vol. 27, no. 4, pp. A17-A18.

Lord, MS, Whitelock, JM, Simmons, A, Williams, RL & Milthorpe, BK 2014, 'Fibrinogen adsorption and platelet adhesion to silica surfaces with stochastic nanotopography', Biointerphases, vol. 9, no. 4, pp. 041002-041002.
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In this study, the effect of surface nanoscale roughness on fibrinogen adsorption and platelet adhesion was investigated. Nanorough silica surfaces with a low level of surface roughness (10 nm Rrms) were found to support the same level of fibrinogen adsorption as the planar silica surfaces, while nanorough silica surfaces with higher levels of surface roughness (15 nm Rrms) were found to support significantly less fibrinogen adsorption. All surfaces analyzed were found to support the same level of platelet adhesion; however, platelets were rounded in morphology on the nanorough silica surfaces while platelets were spread with a well-developed actin cytoskeleton on the planar silica. Unique quartz crystal microbalance with dissipation monitoring (QCM-D) responses was observed for the interactions between platelets and each of the surfaces. The QCM-D data indicated that platelets were more weakly attached to the nanorough silica surfaces compared with the planar silica. These data support the role of surface nanotopography in directing platelet–surface interactions even when the adsorbed fibrinogen layer is able to support the same level of platelet adhesion.

Lu, A, Chen, Y, Li, H, Dowd, A, Cortie, MB, Xie, Q, Guo, H, Qi, Q & Peng, D-L 2014, 'Magnetic metal phosphide nanorods as effective hydrogen-evolution electrocatalysts', INTERNATIONAL JOURNAL OF HYDROGEN ENERGY, vol. 39, no. 33, pp. 18919-18928.
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Lu, J, Turnbull, L, Burke, CM, Liu, M, Carter, DA, Schlothauer, RC, Whitchurch, CB & Harry, EJ 2014, 'Manuka-type honeys can eradicate biofilms produced by Staphylococcus aureus strains with different biofilm-forming abilities', PEERJ, vol. 2, no. 1.
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Chronic wounds are a major global health problem. Their management is difficult and costly, and the development of antibiotic resistance by both planktonic and biofilm-associated bacteria necessitates the use of alternative wound treatments. Honey is now being revisited as an alternative treatment due to its broad-spectrum antibacterial activity and the inability of bacteria to develop resistance to it. Many previous antibacterial studies have used honeys that are not well characterized, even in terms of quantifying the levels of the major antibacterial components present, making it difficult to build an evidence base for the efficacy of honey as an antibiofilm agent in chronic wound treatment. Here we show that a range of well-characterized New Zealand manuka-type honeys, in which two principle antibacterial components, methylglyoxal and hydrogen peroxide, were quantified, can eradicate biofilms of a range of Staphylococcus aureus strains that differ widely in their biofilm-forming abilities. Using crystal violet and viability assays, along with confocal laser scanning imaging, we demonstrate that in all S. aureus strains, including methicillin-resistant strains, the manuka-type honeys showed significantly higher anti-biofilm activity than clover honey and an isotonic sugar solution.We observed higher anti-biofilm activity as the proportion of manuka-derived honey, and thus methylglyoxal, in a honey blend increased. However, methylglyoxal on its own, or with sugar, was not able to effectively eradicate S. aureus biofilms.We also demonstrate that honey was able to penetrate through the biofilm matrix and kill the embedded cells in some cases. As has been reported for antibiotics, sub-inhibitory concentrations of honey improved biofilm formation by some S. aureus strains, however, biofilm cell suspensions recovered after honey treatment did not develop resistance towards manukatype honeys. New Zealand manuka-type honeys, at the concentrations they can be...

Lu, Y, Lu, J, Zhao, J, Cusido, J, Raymo, FM, Yuan, J, Yang, S, Leif, RC, Huo, Y, Piper, JA, Paul Robinson, J, Goldys, EM & Jin, D 2014, 'On-the-fly decoding luminescence lifetimes in the microsecond region for lanthanide-encoded suspension arrays', Nature Communications, vol. 5, no. 1, pp. 1-8.
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Significant multiplexing capacity of optical time-domain coding has been recently demonstrated by tuning luminescence lifetimes of the upconversion nanoparticles called 'τ-Dots'. It provides a large dynamic range of lifetimes from microseconds to milliseconds, which allows creating large libraries of nanotags/microcarriers. However, a robust approach is required to rapidly and accurately measure the luminescence lifetimes from the relatively slow-decaying signals. Here we show a fast algorithm suitable for the microsecond region with precision closely approaching the theoretical limit and compatible with the rapid scanning cytometry technique.We exploit this approach to further extend optical time-domain multiplexing to the downconversion luminescence, using luminescence microspheres wherein lifetimes are tuned through luminescence resonance energy transfer.We demonstrate real-time discrimination of these microspheres in the rapid scanning cytometry, and apply them to the multiplexed probing of pathogen DNA strands. Our results indicate that tunable luminescence lifetimes have considerable potential in high-throughput analytical sciences. © 2014 Macmillan Publishers Limited. All rights reserved.

Lu, Y, Zhao, J, Zhang, R, Liu, Y, Liu, D, Goldys, EM, Yang, X, Xi, P, Sunna, A, Lu, J, Shi, Y, Leif, RC, Huo, Y, Shen, J, Piper, JA, Robinson, JP & Jin, D 2014, 'Tunable lifetime multiplexing using luminescent nanocrystals', Nature Photonics, vol. 8, no. 1, pp. 32-36.
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Optical multiplexing plays an important role in applications such as optical data storage, document security, molecular probes and bead assays for personalized medicine. Conventional fluorescent colour coding is limited by spectral overlap and background interference, restricting the number of distinguishable identities. Here, we show that tunable luminescent lifetimes τ in the microsecond region can be exploited to code individual upconversion nanocrystals. In a single colour band, one can generate more than ten nanocrystal populations with distinct lifetimes ranging from 25.6 μs to 662.4 μs and decode their well-separated lifetime identities, which are independent of both colour and intensity. Such 'τ-dots' potentially suit multichannel bioimaging, high-throughput cytometry quantification, high-density data storage, as well as security codes to combat counterfeiting. This demonstration extends the optical multiplexing capability by adding the temporal dimension of luminescent signals, opening new opportunities in the life sciences, medicine and data security. © 2013 Macmillan Publishers Limited. All rights reserved.

Lund, ME, O'Brien, BA, Hutchinson, AT, Robinson, MW, Simpson, AM, Dalton, JP & Donnelly, S 2014, 'Secreted Proteins from the Helminth Fasciola hepatica Inhibit the Initiation of Autoreactive T Cell Responses and Prevent Diabetes in the NOD Mouse', PLOS ONE, vol. 9, no. 1, p. e86289.
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Infections with helminth parasites prevent/attenuate auto-inflammatory disease. Here we show that molecules secreted by a helminth parasite could prevent Type 1 Diabetes (T1D) in nonobese diabetic (NOD) mice. When delivered at 4 weeks of age (coincident with the initiation of autoimmunity), the excretory/secretory products of Fasciola hepatica (FhES) prevented the onset of T1D, with 84% of mice remaining normoglycaemic and insulitis-free at 30 weeks of age. Disease protection was associated with suppression of IFN-γ secretion from autoreactive T cells and a switch to the production of a regulatory isotype (from IgG2a to IgG1) of autoantibody. Following FhES injection, peritoneal macrophages converted to a regulatory M2 phenotype, characterised by increased expression levels of Ym1, Arg-1, TGFb and PD-L1. Expression of these M2 genetic markers increased in the pancreatic lymph nodes and the pancreas of FhES-treated mice. In vitro , FhES-stimulated M2 macrophages induced the differentiation of Tregs from splenocytes isolated from naïve NOD mice. Collectively, our data shows that FhES contains immune-modulatory molecules that mediate protection from autoimmune diabetes via the induction and maintenance of a regulatory immune environment. © 2014 Lund et al.

Luo, J, Zhang, J, Tan, X, McDougald, D, Zhuang, G, Fane, AG, Kjelleberg, S, Cohen, Y & Rice, SA 2014, 'The correlation between biofilm biopolymer composition and membrane fouling in submerged membrane bioreactors', Biofouling, vol. 30, no. 9, pp. 1093-1110.
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© 2014, © 2014 Taylor & Francis. Biofouling, the combined effect of microorganism and biopolymer accumulation, significantly reduces the process efficiency of membrane bioreactors (MBRs). Here, four biofilm components, alpha-polysaccharides, beta-polysaccharides, proteins and microorganisms, were quantified in MBRs. The biomass of each component was positively correlated with the transmembrane pressure increase in MBRs. Proteins were the most abundant biopolymer in biofilms and showed the fastest rate of increase. The spatial distribution and co-localization analysis of the biofouling components indicated at least 60% of the extracellular polysaccharide (EPS) components were associated with the microbial cells when the transmembrane pressure (TMP) entered the jump phase, suggesting that the EPS components were either secreted by the biofilm cells or that the deposition of these components facilitated biofilm formation. It is suggested that biofilm formation and the accumulation of EPS are intrinsically coupled, resulting in biofouling and loss of system performance. Therefore, strategies that control biofilm formation on membranes may result in a significant improvement of MBR performance.

Luong, S & Fu, S 2014, 'Detection and identification of 2-nitro-morphine and 2-nitro- morphine-6-glucuronide in nitrite adulterated urine specimens containing morphine and its glucuronides', DRUG TESTING AND ANALYSIS, vol. 6, no. 3, pp. 277-287.
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In vitro urine adulteration is a well-documented practice adopted by individuals aiming to evade detection of drug use, when required to undergo mandatory sports and workplace drug testing. Potassium nitrite is an effective urine adulterant due to its oxidizing potential, and has been shown to mask the presence of many drugs of abuse. However, limited research has been conducted to understand its mechanism of action, and to explore the possibility of the drugs undergoing direct oxidation to form stable reaction products. In this study, opiates including morphine, codeine, morphine-3-glucuronide and morphine-6-glucuronide were exposed to potassium nitrite in water and urine to mimic the process of nitrite adulteration. It was found that two stable reaction products were detected by liquid chromatography-mass spectrometry (LC-MS) when morphine and morphine-6-glucuronide were exposed to nitrite. Isolation and elucidation using spectrometric and spectroscopic techniques revealed that they were 2-nitro-morphine and 2-nitro-morphine-6-glucuronide, respectively. These reaction products were also formed when an authentic morphine-positive urine specimen was fortified with nitrite. 2-Nitro-morphine was found to be stable enough to undergo the enzymatic hydrolysis procedure and also detectable by gas chromatography-mass spectrometry (GC-MS) after forming a trimethylsilyl derivative. On the contrary, morphine-3-glucuronide did not appear to be chemically manipulated when exposed to potassium nitrite in urine.

Luong, S, Ung, AT, Kalman, J & Fu, S 2014, 'Transformation of codeine and codeine-6-glucuronide to opioid analogues by urine adulteration with pyridinium chlorochromate: potential issue for urine drug testing', RAPID COMMUNICATIONS IN MASS SPECTROMETRY, vol. 28, no. 14, pp. 1609-1620.
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Ma, X, Huete, A, Yu, Q, Restrepo-Coupe, N, Beringer, J, Hutley, LB, Kanniah, KD, Cleverly, J & Eamus, D 2014, 'Parameterization of an ecosystem light-use-efficiency model for predicting savanna GPP using MODIS EVI', REMOTE SENSING OF ENVIRONMENT, vol. 154, no. 1, pp. 253-271.
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© 2014 Elsevier Inc. Accurate estimation of carbon fluxes across space and time is of great importance for quantifying global carbon balances. Current production efficiency models for calculation of gross primary production (GPP) depend on estimates of light-use-efficiency (LUE) obtained from look-up tables based on biome type and coarse-resolution meteorological inputs that can introduce uncertainties. Plant function is especially difficult to parameterize in the savanna biome due to the presence of varying mixtures of multiple plant functional types (PFTs)with distinct phenologies and responses to environmental factors. The objective of this study was to find a simple and robust method to accurately up-scale savanna GPP fromlocal, eddy covariance (EC) flux tower GPP measures to regional scales utilizing entirely remote sensing oservations. Here we assessed seasonal patterns of Moderate Resolution Imaging Spectroradiometer (MODIS) vegetation productswith seasonal EC tower GPP (GPPEC) at four sites along an ecological rainfall gradient (the North Australian Tropical Transect, NATT) encompassing tropical wet to dry savannas. The enhanced vegetation index (EVI) tracked the seasonal variations of GPPEC well at both site- and cross-site levels (R2= 0.84). The EVI relationship with GPPEC was further strengthened through coupling with ecosystem light-use-efficiency (eLUE), defined as the ratio of GPP to photosynthetically active radiation (PAR). Two savanna landscape eLUEmodels, driven by top-of-canopy incident PAR (PARTOC) or top-of-atmosphere incident PAR (PARTOA) were parameterized and investigated. GPP predicted using the eLUE models correlated well with GPPEC, with R2 of 0.85 (RMSE = 0.76 g C m-2 d-1) and 0.88 (RMSE = 0.70 g C m-2 d-1) for PARTOC and PARTOA, respectively, and were significantly improved compared to the MOD17 GPP product (R2 = 0.58, RMSE= 1.43 g C m-2 d-1). The eLUE model also minimized the seasonal hysteresis observed between greenup and...

Macreadie, PI, Baird, ME, Trevathan-Tackett, SM, Larkum, AWD & Ralph, PJ 2014, 'Quantifying and modelling the carbon sequestration capacity of seagrass meadows - A critical assessment', MARINE POLLUTION BULLETIN, vol. 83, no. 2, pp. 430-439.
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Seagrasses are among the planet's most effective natural ecosystems for sequestering (capturing and storing) carbon (C); but if degraded, they could leak stored C into the atmosphere and accelerate global warming. Quantifying and modelling the C sequestration capacity is therefore critical for successfully managing seagrass ecosystems to maintain their substantial abatement potential. At present, there is no mechanism to support carbon financing linked to seagrass. For seagrasses to be recognised by the IPCC and the voluntary C market, standard stock assessment methodologies and inventories of seagrass C stocks are required. Developing accurate C budgets for seagrass meadows is indeed complex; we discuss these complexities, and, in addition, we review techniques and methodologies that will aid development of C budgets. We also consider a simple process-based data assimilation model for predicting how seagrasses will respond to future change, accompanied by a practical list of research priorities. © 2013 Elsevier Ltd.

Magyar, A, Hu, W, Shanley, T, Flatte, ME, Hu, E & Aharonovich, I 2014, 'Synthesis of luminescent europium defects in diamond', NATURE COMMUNICATIONS, vol. 5, pp. 1-6.
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© 2014 Macmillan Publishers Limited. All rights reserved. Lanthanides are vital components in lighting, imaging technologies and future quantum memory applications owing to their narrow optical transitions and long spin coherence times. Recently, diamond has become a pre-eminent platform for the realisation of many experiments in quantum information science. Here we demonstrate a promising approach to incorporate Eu ions into diamond, providing a means to harness the exceptional characteristics of both lanthanides and diamond in a single material. Polyelectrolytes are used to electrostatically assemble Eu(III) chelate molecules on diamond and subsequently chemical vapour deposition is employed for the diamond growth. Fluorescence measurements show that the Eu atoms retain the characteristic optical signature of Eu(III) upon incorporation into the diamond lattice. Computational modelling supports the experimental findings, corroborating that Eu(III) in diamond is a stable configuration. The formed defects demonstrate the outstanding chemical control over the incorporation of impurities into diamond enabled by the electrostatic assembly together with chemical vapour deposition growth.

Magyar, AP, Bracher, D, Lee, JC, Aharonovich, I & Hu, EL 2014, 'High quality SiC microdisk resonators fabricated from monolithic epilayer wafers', APPLIED PHYSICS LETTERS, vol. 104, no. 5, pp. 051109-1-051109 -3.
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The exquisite mechanical properties of SiC have made it an important industrial material with applications in microelectromechanical devices and high power electronics. Recently, the optical properties of SiC have garnered attention for applications in photonics, quantum information, and spintronics. This work demonstrates the fabrication of microdisks formed from a p-N SiC epilayer material. The microdisk cavities fabricated from the SiC epilayer material exhibit quality factors of as high as 9200 and the approach is easily adaptable to the fabrication of SiC-based photonic crystals and other photonic and optomechanical devices. © 2014 AIP Publishing LLC.

Maity, A, Williams, PL, Ryan, L, Missmer, SA, Coull, BA & Hauser, R 2014, 'Analysis of in vitro fertilization data with multiple outcomes using discrete time-to-event analysis', STATISTICS IN MEDICINE, vol. 33, no. 10, pp. 1738-1749.
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Makume, BF, Bredenkamp, T & Williams, DBG 2014, 'Substrate Requirements for Palladium–Aluminium Triflate Co‐catalysed Hydromethoxycarbonylation Reactions of Alkynes Bearing Oxygen Atoms', ChemCatChem, vol. 6, no. 10, pp. 2801-2804.
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AbstractThe palladium diacetate–aluminium triflate combination is an effective catalyst for the hydromethoxycarbonylation reaction of isolated alkenes and alkynes. However, its application in the hydromethoxycarbonylation of oxygen atom‐bearing alkynes is non‐trivial: the position relative to the alkyne (e.g., allylic, homoallylic) and nature of the oxygen atom determine the success of the transformation. We detail the minimum structural requirements for a successful outcome with ether‐containing alkyne substrates and hydroxyl‐containing analogues. In general, the oxygen atom has a detrimental effect on the outcome of the hydromethoxycarbonylation reaction, which can be overcome in many instances. The presence of the oxygen atom(s) causes decreases in the rate of the reaction compared to aliphatic alkynes and the closer the oxygen atom is to the triple bond, the more pronounced the effect. The chemistry is demonstrated on complex substrates derived from 5 and 6‐carbon sugars in optimised reactions.

Maltby, S, Hansbro, NG, Tay, HL, Stewart, J, Plank, M, Donges, B, Rosenberg, HF & Foster, PS 2014, 'Production and Differentiation of Myeloid Cells Driven by Proinflammatory Cytokines in Response to Acute Pneumovirus Infection in Mice', The Journal of Immunology, vol. 193, no. 8, pp. 4072-4082.
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Abstract Respiratory virus infections are often pathogenic, driving severe inflammatory responses. Most research has focused on localized effects of virus infection and inflammation. However, infection can induce broad-reaching, systemic changes that are only beginning to be characterized. In this study, we assessed the impact of acute pneumovirus infection in C57BL/6 mice on bone marrow hematopoiesis. We hypothesized that inflammatory cytokine production in the lung upregulates myeloid cell production in response to infection. We demonstrate a dramatic increase in the percentages of circulating myeloid cells, which is associated with pronounced elevations in inflammatory cytokines in serum (IFN-γ, IL-6, CCL2), bone (TNF-α), and lung tissue (TNF-α, IFN-γ, IL-6, CCL2, CCL3, G-CSF, osteopontin). Increased hematopoietic stem/progenitor cell percentages (Lineage−Sca-I+c-kit+) were also detected in the bone marrow. This increase was accompanied by an increase in the proportions of committed myeloid progenitors, as determined by colony-forming unit assays. However, no functional changes in hematopoietic stem cells occurred, as assessed by competitive bone marrow reconstitution. Systemic administration of neutralizing Abs to either TNF-α or IFN-γ blocked expansion of myeloid progenitors in the bone marrow and also limited virus clearance from the lung. These findings suggest that acute inflammatory cytokines drive production and differentiation of myeloid cells in the bone marrow by inducing differentiation of committed myeloid progenitors. Our findings provide insight into the mechanisms via which innate immune responses regulate myeloid cell progenitor numbers in response to acute respiratory virus infection.

Maniam, S, Higginbotham, HF, Guo, S, Bell, TDM, Izgorodina, EI & Langford, SJ 2014, 'A Redox Switchable Dihydrobenzo[b]pyrazine Push‐Pull System', Asian Journal of Organic Chemistry, vol. 3, no. 5, pp. 619-623.
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AbstractThe synthesis and spectroscopic properties of a dissymmetrically core‐extended naphthalene diimides derived from o‐phenylenediamine and cyanoethene dithiolate were explored. The push‐pull nature of the peripheral substituents allows these naphthalene diimide dyes and their progenitors to display interesting photophysical and electrochemical properties, with the target system acting as a highly reversible and quantitative molecular switch with clear absorption and emission readouts based on chemical oxidation and reduction processes.

Marlton, FP, Goossens, DJ, White, R & Hutchison, WD 2014, 'Rapid Microwave Synthesis and Structural Phase Diagram of Ln_xY_1−xMnO₃', Zeitschrift für Naturforschung B, vol. 69, no. 7, pp. 761-766.
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YMnO3 is one of the primary examples of a multiferroic ceramic. We present a novel solid-state microwave sintering method for making high-purity ceramic samples of YMnO3 and related compounds in a few hours. This leads to determination of the structural phase diagram for the formation of single-phase, hexagonal samples when doping lanthanides into YMnO3. It is found that the solidstate microwave synthesis allows manufacture of high-quality samples in hours rather than days. The resulting phase diagram accords well with results from the literature, and from calculations based on the Goldschmidt tolerance factor for the stability of perovskite structures, suggesting that the transformation from hexagonal to perovskite with doping is driven essentially by ion sizes. Some results concerning the microwave synthesis of BaLnInO4 compounds, where Ln is a lanthanide, are noted. Microwave sintering of BaNdInO4 yields single-phase samples where conventional sintering does not.

Marriott, C, Lee, R, Wilkes, Z, Comber, B, Spindler, X, Roux, C & Lennard, C 2014, 'Evaluation of fingermark detection sequences on paper substrates', FORENSIC SCIENCE INTERNATIONAL, vol. 236, pp. 30-37.
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It is generally accepted that the amino acid reagent consisting of 1,2-indanedione and a catalytic amount of zinc chloride, referred to as IND-Zn, is the single best method for the detection of latent fingermarks on paper substrates and that ninhydrin is of limited value when used in sequence after this reagent. However, recent research has suggested that the sequence 1,8-diazafluoren-9-one (DFO) followed by ninhydrin may actually produce a greater number of fingermarks than IND-Zn on its own or IND-Zn followed by ninhydrin.This study focussed on the evaluation of two fingermark detection sequences for porous surfaces: (1) IND-Zn followed by ninhydrin, physical developer (PD) and the lipid stain nile red; and (2) DFO followed by ninhydrin, PD and nile red. The evaluation was undertaken using a range of latent fingermark donors and on a number of paper substrates that are commonly encountered in Australia. In addition, a pseudo-operational trial was completed on 5-year-old university examination booklets. Parallel studies were undertaken at two locations: Sydney (temperate, coastal climate) and Canberra (relatively dry, continental climate).The results of the donor study indicated that there was a negligible difference in performance between the two sequences across all paper types and all time periods evaluated. When considering individual reagents, IND-Zn generally developed better quality fingermarks compared to DFO; however, ninhydrin had a greater enhancement effect on DFO developed marks than after IND-Zn. In the pseudo-operational trials, the IND-Zn sequence outperformed the DFO sequence. Nile red did not develop any additional marks at the end of each sequence and, as a result, the use of this technique at the end of a full sequence is of questionable value.The overall outcome was that the sequence IND-Zn followed by ninhydrin and PD is recommended for the processing of common paper substrates under the conditions typically experienced at the two...

Marsh, DJ, Shah, JS & Cole, AJ 2014, 'Histones and Their Modifications in Ovarian Cancer – Drivers of Disease and Therapeutic Targets', Frontiers in Oncology, vol. 4.
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Epithelial ovarian cancer has the highest mortality of the gynecological malignancies. High grade serous epithelial ovarian cancer (SEOC) is the most common subtype, with the majority of women presenting with advanced disease where 5-year survival is around 25%. Platinum-based chemotherapy in combination with paclitaxel remains the most effective treatment despite platinum therapies being introduced almost 40 years ago. Advances in molecular medicine are underpinning new strategies for the treatment of cancer. Major advances have been made by international initiatives to sequence cancer genomes. For SEOC, with the exception of TP53 that is mutated in virtually 100% of these tumors, there is no other gene mutated at high frequency. There is extensive copy number variation, as well as changes in methylation patterns that will influence gene expression. To date, the role of histones and their post-translational modifications in ovarian cancer is a relatively understudied field. Post-translational histone modifications play major roles in gene expression as they direct the configuration of chromatin and so access by transcription factors. Histone modifications include methylation, acetylation, and monoubiquitination, with involvement of enzymes including histone methyltransferases, histone acetyltransferases/deacetylases, and ubiquitin ligases/deubiquitinases, respectively. Complexes such as the Polycomb repressive complex also play roles in the control of histone modifications and more recently roles for long non-coding RNA and microRNAs are emerging. Epigenomic-based therapies targeting histone modifications are being developed and offer new approaches for the treatment of ovarian cancer. Here, we discuss histone modifications and their aberrant regulation in malignancy and specifically in ovarian cancer. We review current and upcoming histone-based therapies that have the potential to inform and improve treatment strategies for women with ovarian cancer.

Martin, AA & Toth, M 2014, 'Cryogenic Electron Beam Induced Chemical Etching', ACS APPLIED MATERIALS & INTERFACES, vol. 6, no. 21, pp. 18457-18460.
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© 2014 American Chemical Society. Cryogenic cooling is used to enable efficient, gas-mediated electron beam induced etching (EBIE) in cases where the etch rate is negligible at room and elevated substrate temperatures. The process is demonstrated using nitrogen trifluoride (NF3) as the etch precursor, and Si, SiO2, SiC, and Si3N4 as the materials volatilized by an electron beam. Cryogenic cooling broadens the range of precursors that can be used for EBIE, and enables high-resolution, deterministic etching of materials that are volatilized spontaneously by conventional etch precursors as demonstrated here by NF3 and XeF2 EBIE of silicon.

Martin, AA, Aharonovich, I & Toth, M 2014, 'Gas-Mediated Electron Beam Induced Etching - From Fundamental Physics to Device Fabrication', Microscopy and Microanalysis, vol. 20, no. S3, pp. 364-365.
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Gas-mediated electron beam induced etching (EBIE) is a nanoscale, direct-write technique analogous to gas-assisted focused ion beam (FIB) milling. The main advantage of EBIE is the elimination of sputtering and ion implantation during processing as well as greater material selectivity [1]. Here we discuss recent developments that expand the scope of EBIE applications in nanofabrication and defect generation analysis, and show advances in hardware that open the door for new studies in reaction kinetics using a scanning electron microscope (SEM).

Martin, AA, Toth, M & Aharonovich, I 2014, 'Subtractive 3D Printing of Optically Active Diamond Structures', SCIENTIFIC REPORTS, vol. 4.
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Controlled fabrication of semiconductor nanostructures is an essential step in engineering of high performance photonic and optoelectronic devices. Diamond in particular has recently attracted considerable attention as a promising platform for quantum technologies, photonics and high resolution sensing applications. Here we demonstrate the fabrication of optically active, functional diamond structures using gas-mediated electron beam induced etching (EBIE). The technique achieves dry chemical etching at room temperature through the dissociation of surface-adsorbed H2O molecules by energetic electrons in a water vapor environment. Parallel processing is possible by electron flood exposure and the use of an etch mask, while high resolution, mask-free, iterative editing is demonstrated by direct write etching of inclined facets of diamond microparticles. The realized structures demonstrate the potential of EBIE for the fabrication of optically active structures in diamond.

Martinac, B, Nomura, T, Chi, G, Petrov, E, Rohde, PR, Battle, AR, Foo, A, Constantine, M, Rothnagel, R, Carne, S, Deplazes, E, Cornell, B, Cranfield, CG, Hankamer, B & Landsberg, MJ 2014, 'Bacterial Mechanosensitive Channels: Models for Studying Mechanosensory Transduction', ANTIOXIDANTS & REDOX SIGNALING, vol. 20, no. 6, pp. 952-969.
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Significance: Sensations of touch and hearing are manifestations of mechanical contact and air pressure acting on touch receptors and hair cells of the inner ear, respectively. In bacteria, osmotic pressure exerts a significant mechanical force on their cellular membrane. Bacteria have evolved mechanosensitive (MS) channels to cope with excessive turgor pressure resulting from a hypo-osmotic shock. MS channel opening allows the expulsion of osmolytes and water, thereby restoring normal cellular turgor and preventing cell lysis. Recent Advances: As biological force-sensing systems, MS channels have been identified as the best examples of membrane proteins coupling molecular dynamics to cellular mechanics. The bacterial MS channel of large conductance (MscL) and MS channel of small conductance (MscS) have been subjected to extensive biophysical, biochemical, genetic, and structural analyses. These studies have established MscL and MscS as model systems for mechanosensory transduction. Critical Issues: In recent years, MS ion channels in mammalian cells have moved into focus of mechanotransduction research, accompanied by an increased awareness of the role they may play in the pathophysiology of diseases, including cardiac hypertrophy, muscular dystrophy, or Xerocytosis. Future Directions: A recent exciting development includes the molecular identification of Piezo proteins, which function as nonselective cation channels in mechanosensory transduction associated with senses of touch and pain. Since research on Piezo channels is very young, applying lessons learned from studies of bacterial MS channels to establishing the mechanism by which the Piezo channels are mechanically activated remains one of the future challenges toward a better understanding of the role that MS channels play in mechanobiology. Antioxid. Redox Signal. 20, 952-969. © 2014 Mary Ann Liebert, Inc.

MASLOVSKAYA, O, BROWN, JJ, SMITH, PWF & PADMADAS, SS 2014, 'HIV AWARENESS IN CHINA AMONG WOMEN OF REPRODUCTIVE AGE (1997–2005): A DECOMPOSITION ANALYSIS', Journal of Biosocial Science, vol. 46, no. 2, pp. 178-198.
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SummaryHIV prevalence in China is less than one per cent, but the absolute number of people living with HIV/AIDS is large and growing. Given the limited scope of any potential cure for HIV, prevention plays a crucial role in controlling the epidemic. This paper examines the evolution of HIV awareness among women in China between 1997 and 2005. A regression decomposition analysis technique was used to disentangle the two main components driving a change in HIV awareness. The results show that HIV awareness has increased over time in China. The gaps between groups are narrowing over time and lower HIV awareness groups are catching up with the higher awareness groups. In 2005 education remained one of the main factors associated with HIV awareness, the other main factors being ethnicity, exposure to TV and newspapers. The increases in HIV awareness observed between 1997 and 2001 are similar between groups of women with different demographic characteristics, whereas between 2003 and 2005 increases are more pronounced among specific groups of women such as women from rural areas, women from Western parts of the country, women who belong to ethnic minorities and those with no education or with only primary education. The results suggest that the main driver of the observed change in HIV awareness over time in China is change in the environment such as in political commitment, interventions and campaigns rather than change in population structure.

Mazel, D, Colwell, R, Klose, K, Oliver, J, Crumlish, M, McDougald, D, Bland, MJ & Austin, B 2014, 'VIBRIO 2014 meeting report', Research in Microbiology, vol. 165, no. 10, pp. 857-864.
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McCord, B 2014, 'Forensic Analysis', ELECTROPHORESIS, vol. 35, no. 21-22, pp. 3019-3019.
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McElroy, KE, Hui, JGK, Woo, JKK, Luk, AWS, Webb, JS, Kjelleberg, S, Rice, SA & Thomas, T 2014, 'Strain-specific parallel evolution drives short-term diversification during Pseudomonas aeruginosa biofilm formation', Proceedings of the National Academy of Sciences, vol. 111, no. 14, pp. E1419-E1427.
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Significance Within-population genetic diversity is an essential evolutionary prerequisite for processes ranging from antibiotic resistance to niche adaptation, but its generation is poorly understood, with most studies focusing on fixed substitutions at the end point of long-term evolution. Using deep sequencing, we analyzed short-term, within-population genetic diversification occurring during biofilm formation of the model bacterium Pseudomonas aeruginosa . We discovered extensive parallel evolution between biological replicates at the level of pathways, genes, and even individual nucleotides. Short-term diversification featured positive selection of relatively few nonsynonymous mutations, with the majority of the genome being conserved by negative selection. This result is broadly consistent with observations of long-term evolution and suggests diversifying selection may underlie genetic diversification of Pseudomonas aeruginosa biofilms.

McGowan, N, Fowler, AM, Parkinson, K, Bishop, DP, Ganio, K, Doble, PA, Booth, DJ & Hare, DJ 2014, 'Beyond the transect: An alternative microchemical imaging method for fine scale analysis of trace elements in fish otoliths during early life', SCIENCE OF THE TOTAL ENVIRONMENT, vol. 494, pp. 177-186.
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© 2014 Elsevier B.V. Microchemical analysis of otolith (calcified 'ear stones' used for balance and orientation) of fishes is an important tool for studying their environmental history and management. However, the spatial resolution achieved is often too coarse to examine short-term events occurring in early life. Current methods rely on single points or transects across the otolith surface, which may provide a limited view of elemental distributions, a matter that has not previously been investigated. Imaging by laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) permits microchemical analyses of short-term events in early life with high (<10μm) resolution, two-dimensional (2D) visualization of elemental distributions. To demonstrate the potential of this method, we mapped the concentrations of Sr and Ba, two key trace elements, in a small number of juvenile otoliths of neon damselfish (Pomacentrus coelestis) using an 8μm beam diameter (laser fluence of 13.8±3.5Jcm-2). Quantification was performed using the established method by Longerich et al. (1996), which is applied to 2D imaging of a biological matrix here for the first time. Accuracy of >97% was achieved using a multi-point non matrix-matched calibration of National Institute of Standards and Technology (NIST) 610 and 612 (trace elements in glass) using Longerich's calculation method against the matrix-matched standard FEBS-1 (powdered red snapper [Lutjanus campechanus] otolith). The spatial resolution achieved in the otolith corresponded to a time period of 2±1days during the larval phase, and 4±1days during the post-settlement juvenile phase. This method has the potential to improve interpretations of early life-history events at scales corresponding to specific events. While the images showed gradients in Sr and Ba across the larval settlement zone more clearly than single transects, the method proved sample homogeneity throughout the structure; demonstrating that 2D sc...

McGrath, KC, Li, XH, Whitworth, PT, Kasz, R, Tan, JT, McLennan, SV, Celermajer, DS, Barter, PJ, Rye, K-A & Heather, AK 2014, 'High density lipoproteins improve insulin sensitivity in high-fat diet-fed mice by suppressing hepatic inflammation', Journal of Lipid Research, vol. 55, no. 3, pp. 421-430.
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Obesity-induced liver inflammation can drive insulin resistance. HDL has anti-inflammatory properties, so we hypothesized that low levels of HDL would perpetuate inflammatory responses in the liver and that HDL treatment would suppress liver inflammation and insulin resistance. The aim of this study was to investigate the effects of lipid-free apoAI on hepatic inflammation and insulin resistance in mice. We also investigated apoAI as a component of reconstituted HDLs (rHDLs) in hepatocytes to confirm results we observed in vivo. To test our hypothesis, C57BL/6 mice were fed a high-fat diet (HFD) for 16 weeks and administered either saline or lipid-free apoAI. Injections of lipid-free apoAI twice a week for 2 or 4 weeks with lipid-free apoAI resulted in: i) improved insulin sensitivity associated with decreased systemic and hepatic inflammation; ii) suppression of hepatic mRNA expression for key transcriptional regulators of lipogenic gene expression; and iii) suppression of nuclear factor κB (NF-κB) activation. Human hepatoma HuH-7 cells exposed to rHDLs showed suppressed TNFα-induced NF-κB activation, correlating with decreased NF-κB target gene expression. We conclude that apoAI suppresses liver inflammation in HFD mice and improves insulin resistance via a mechanism that involves a downregulation of NF-κB activation. Copyright © 2014 by the American Society for Biochemistry and Molecular Biology, Inc.

McGrath, KCY, Li, X & Heather, AK 2014, 'Apolipoporotein A-I mimetic peptides improved insulin sensitivity in high fat diet fed mice', Obesity Research & Clinical Practice, vol. 8, pp. 64-65.
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McIlroy, DJ, Jarnicki, AG, Au, GG, Lott, N, Smith, DW, Hansbro, PM & Balogh, ZJ 2014, 'Mitochondrial DNA neutrophil extracellular traps are formed after trauma and subsequent surgery', Journal of Critical Care, vol. 29, no. 6, pp. 1133.e1-1133.e5.
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Introduction

Neutrophil extracellular traps (NETs) have not been demonstrated after trauma and subsequent surgery. Neutrophil extracellular traps are formed from pure mitochondrial DNA (mtDNA) under certain conditions, which is potently proinflammatory. We hypothesized that injury and orthopedic trauma surgery would induce NET production with mtDNA as a structural component.

Methods

Neutrophils were isolated 8 trauma patients requiring orthopedic surgery postinjury and up to 5 days postoperatively. Four healthy volunteers provided positive and negative controls. Total hip replacement patients acted as an uninjured surgical control group. Neutrophil extracellular traps were visualized with DNA (Hoechst 33342TM/Sytox Green/MitoSox/MitoTracker) stains using live cell fluorescence microscopy with downstream quantitative polymerase chain reaction analysis of DNA composition.

Results

Neutrophil extracellular traps were present after injury in all 8 trauma patients. They persisted for 5 days postoperatively. Delayed surgery resulted in NET resolution, but they reformed postoperatively. Total hip replacement patients developed NETs postoperatively, which resolved by day 5. Quantitative polymerase chain reaction analysis of NET-DNA composition revealed that NETs formed after injury and surgery were made of mtDNA with no detectable nuclear DNA component.

Conclusions

Neutrophil extracellular traps formed after major trauma and subsequent surgery contain mtDNA and represent a novel marker of heightened innate immune activation. They could be considered when timing surgery after trauma to prevent systemic NET-induced inflammatory complications.

McLaughlin, J, Nelson, M, McNevin, D, Roffey, P & Gahan, ME 2014, 'Characterization of Bacillus strains and hoax agents by protein profiling using automated microfluidic capillary electrophoresis', Forensic Science, Medicine, and Pathology, vol. 10, no. 3, pp. 380-389.
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McPherson, DJ, Supansomboon, S, Zwan, B, Keast, VJ, Cortie, DL, Gentle, A, Dowd, A & Cortie, MB 2014, 'Strategies to control the spectral properties of Au-Ni thin films', THIN SOLID FILMS, vol. 551, pp. 200-204.
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Metcalf, BJ, Spring, JB, Humphreys, PC, Thomas-Peter, N, Barbieri, M, Kolthammer, WS, Jin, X-M, Langford, NK, Kundys, D, Gates, JC, Smith, BJ, Smith, PGR & Walmsley, IA 2014, 'Quantum teleportation on a photonic chip', Nature Photonics, vol. 8, no. 10, pp. 770-774.
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Middleburgh, SC, King, DM, Lumpkin, GR, Cortie, M & Edwards, L 2014, 'Segregation and migration of species in the CrCoFeNi high entropy alloy', JOURNAL OF ALLOYS AND COMPOUNDS, vol. 599, pp. 179-182.
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The formation and migration of intrinsic defects in the CrCoFeNi high entropy alloy has been investigated using ab-initio modeling. The ease of vacancy formation was found to vary depending on the element: vacancies formed by the removal of Fe, Ni and Co are positive while Cr has a negative vacancy formation energy and will precipitate out of the CrCoFeNi alloy. This mechanism may allow the formation of a corrosion passivating oxide layer, analogous to Cr behaviour in stainless steels. The migration and behaviour of intrinsic interstitial defects has also been investigated. © 2014 Published by Elsevier B.V. All rights reserved.

Mitrovic, SM, Westhorpe, DP, Kobayashi, T, Baldwin, DS, Ryan, D & Hitchcock, JN 2014, 'Short-term changes in zooplankton density and community structure in response to different sources of dissolved organic carbon in an unconstrained lowland river: evidence for food web support', Journal of Plankton Research, vol. 36, no. 6, pp. 1488-1500.
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Moezzi, A, Cortie, M, Dowd, A & McDonagh, A 2014, 'On the formation of nanocrystalline active zinc oxide from zinc hydroxide carbonate', JOURNAL OF NANOPARTICLE RESEARCH, vol. 16, no. 4.
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Molnar, A, Fu, S, Lewis, J, Allsop, DJ & Copeland, J 2014, 'The detection of THC, CBD and CBN in the oral fluid of Sativex (R) patients using two on-site screening tests and LC-MS/MS', FORENSIC SCIENCE INTERNATIONAL, vol. 238, pp. 113-119.
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Sativex® is an oromucosal spray used to treat spasticity in multiple sclerosis sufferers in some European countries, the United Kingdom, Canada and New Zealand. The drug has also recently been registered by the Therapeutic Goods Administration (TGA) in Australia for treatment of multiple sclerosis. Sativex® contains high concentrations of ?9-tetrahydrocannabinol (THC) and cannabidiol (CBD), with the former being the subject of random roadside drug tests across Australia to detect cannabis use. This pilot study aims to determine whether or not patients taking Sativex® will test positive to THC using these roadside screening tests. Detectable levels of THC, CBD and cannabinol (CBN) in their oral fluid were also confirmed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). The study was a double-blind, placebo controlled design. Oral fluid was tested prior to and immediately after dosing with either Sativex® or placebo at intervals up to 2 h after the dose. Two Sativex® doses were studied. The low dose contained 5.4 mg THC, the high dose 21.6 mg THC. Results indicate that the primary screening test used in Australian roadside drug testing, the DrugWipe® II Twin, often gave a false negative response for THC, even with high concentrations present. However, secondary screening test, Cozart® DDS (used by police after a DrugWipe test gives a positive result), gave true positive results in all cases where patients were being treated with Sativex1. Confirmatory testing showed high concentrations of THC and CBD (>5356 ng/mL THC and >3826 ng/mL CBD) in the oral fluid shortly after dosing and also elevated concentrations of CBN. Levels dropped quickly but remained at detectable concentrations (>67.6 ng/mL) two hours after drug administration. The average concentration ratio of THC/CBD across all positive samples was 1.10 (%RSD 19.9) reflecting the composition of the Sativex® spray. In conclusion, Sativex® users may test positive for THC by roadside drug testing wi...

Monahan, LG, Hajduk, IV, Blaber, SP, Charles, IG & Harry, EJ 2014, 'Coordinating Bacterial Cell Division with Nutrient Availability: a Role for Glycolysis', MBIO, vol. 5, no. 3.
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Cell division in bacteria is driven by a cytoskeletal ring structure, the Z ring, composed of polymers of the tubulin-like protein FtsZ. Z-ring formation must be tightly regulated to ensure faithful cell division, and several mechanisms that influence the positioning and timing of Z-ring assembly have been described. Another important but as yet poorly understood aspect of cell division regulation is the need to coordinate division with cell growth and nutrient availability. In this study, we demonstrated for the first time that cell division is intimately linked to central carbon metabolism in the model Gram-positive bacterium Bacillus subtilis. We showed that a deletion of the gene encoding pyruvate kinase (pyk), which produces pyruvate in the final reaction of glycolysis, rescues the assembly defect of a temperature-sensitive ftsZ mutant and has significant effects on Z-ring formation in wild-type B. subtilis cells. Addition of exogenous pyruvate restores normal division in the absence of the pyruvate kinase enzyme, implicating pyruvate as a key metabolite in the coordination of bacterial growth and division. Our results support a model in which pyruvate levels are coupled to Z-ring assembly via an enzyme that actually metabolizes pyruvate, the E1α subunit of pyruvate dehydrogenase. We have shown that this protein localizes over the nucleoid in a pyruvatedependent manner and may stimulate more efficient Z-ring formation at the cell center under nutrient-rich conditions, when cells must divide more frequently. © 2014 Monahan et al.

Monahan, LG, Liew, ATF, Bottomley, AL & Harry, EJ 2014, 'Division site positioning in bacteria: one size does not fit all', FRONTIERS IN MICROBIOLOGY, vol. 5, no. FEB.
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Spatial regulation of cell division in bacteria has been a focus of research for decades. It has been well studied in two model rod-shaped organisms, Escherichia coli and Bacillus subtilis, with the general belief that division site positioning occurs as a result of the combination of two negative regulatory systems, Min and nucleoid occlusion. These systems influence division by preventing the cytokinetic Z ring from forming anywhere other than midcell. However, evidence is accumulating for the existence of additional mechanisms that are involved in controlling Z ring positioning both in these organisms and in several other bacteria. In some cases the decision of where to divide is solved by variations on a common evolutionary theme, and in others completely different proteins and mechanisms are involved. Here we review the different ways bacteria solve the problem of finding the right place to divide. It appears that a one-size-fits-all model does not apply, and that individual species have adapted a division-site positioning mechanism that best suits their lifestyle, environmental niche and mode of growth to ensure equal partitioning of DNA for survival of the next generation. © 2014 Monahan, Liew, Bottomley and Harry.

Monahan, LG, Turnbull, L, Osvath, SR, Birch, D, Charles, IG & Whitchurch, CB 2014, 'Rapid Conversion of Pseudomonas aeruginosa to a Spherical Cell Morphotype Facilitates Tolerance to Carbapenems and Penicillins but Increases Susceptibility to Antimicrobial Peptides', ANTIMICROBIAL AGENTS AND CHEMOTHERAPY, vol. 58, no. 4, pp. 1956-1962.
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The Gram-negative human pathogen Pseudomonas aeruginosa tolerates high concentrations of β-lactam antibiotics. Despite inhibiting the growth of the organism, these cell wall-targeting drugs exhibit remarkably little bactericidal activity. However, the mechanisms underlying β-lactam tolerance are currently unclear. Here, we show that P. aeruginosa undergoes a rapid en masse transition from normal rod-shaped cells to viable cell wall-defective spherical cells when treated with β-lactams from the widely used carbapenem and penicillin classes. When the antibiotic is removed, the entire population of spherical cells quickly converts back to the normal bacillary form. Our results demonstrate that these rapid population-wide cell morphotype transitions function as a strategy to survive antibiotic exposure. Taking advantage of these findings, we have developed a novel approach to efficiently kill P. aeruginosa by using carbapenem treatment to induce en masse transition to the spherical cell morphotype and then exploiting the relative fragility and sensitivity of these cells to killing by antimicrobial peptides (AMPs) that are relatively inactive against P. aeruginosa bacillary cells. This approach could broaden the repertoire of antimicrobial compounds used to treat P. aeruginosa and serve as a basis for developing new therapeutic agents to combat bacterial infections. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Mondal, AK, Chen, S, Su, D, Liu, H & Wang, G 2014, 'Fabrication and enhanced electrochemical performances of MoO3/graphene composite as anode material for lithium-ion batteries', International Journal of Smart Grid and Clean Energy, vol. 3, no. 2, pp. 142-148.
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Molybdenum trioxide (Mo0#)/graphene composite were prepared by integrating Mo03 and graphene in dimethylformamide (DMF). The morphology and structure of the materials were characterized by X-ray diffraction, field emission scanning electron microscopy and transmission electron microscopy. The electrochemical properties of Mo03/graphene composite with different ratios were studied as anode materials for lithium-ion batteries using galavanostatic charge-discharge and cyclic voltammetry. We observed that the Mo03/graphene anode with a weight ratio of 1:1 (Mo03 graphene) exhibits a high lithium storage capacity of 967 mA h g-1 at the current density of 500 mA g-1, satisfactory cycling stability and good rate capability.

Mondal, AK, Su, D, Chen, S, Sun, B, Li, K & Wang, G 2014, 'A simple approach to prepare nickel hydroxide nanosheets for enhanced pseudocapacitive performance', RSC ADVANCES, vol. 4, no. 37, pp. 19476-19481.
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Nickel hydroxide nanosheets were synthesized by a simple microwave assisted heating method and investigated as electrochemical pseudo-capacitive materials for supercapacitors. The crystalline structure and morphology of the as-obtained Ni(OH)2 nanosheets were characterized by X-ray diffraction, nitrogen adsorption-desorption isotherms, field emission scanning electron microscopy and transmission electron microscopy. The electrochemical properties of the Ni(OH)2 nanosheets were evaluated by cyclic voltammetry and chronopotentiometry technology in 2 M KOH solution. The nickel hydroxide nanosheet electrode shows a maximum specific capacitance of 2570 F g -1 at a current density of 5 A g-1 and exhibits superior cycling stability. These results suggest its potential application as an electrode material for supercapacitors. © the Partner Organisations 2014.

Mondal, AK, Su, D, Chen, S, Xie, X & Wang, G 2014, 'Highly Porous NiCo₂O₄ Nanoflakes and Nanobelts as Anode Materials for Lithium-Ion Batteries with Excellent Rate Capability', ACS Applied Materials & Interfaces, vol. 6, no. 17, pp. 14827-14835.
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Mondal, AK, Su, D, Chen, S, Zhang, J, Ung, A & Wang, G 2014, 'Microwave-assisted synthesis of spherical β-Ni(OH) 2 superstructures for electrochemical capacitors with excellent cycling stability', Chemical Physics Letters, vol. 610-611, pp. 115-120.
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A novel single-step microwave-assisted process has been developed to synthesize spherical β-Ni(OH)2 superstructures without using any templates. Structure characterizations show that the spherical β-Ni(OH)2 composed of twisted nanosheets was obtained. The electrochemical properties of the as-prepared materials were evaluated by cyclic voltammetry and chronopotentiometry technology in 2 M KOH solution. Due to the unique morphology, the prepared β-Ni(OH)2 electrode displays a high specific capacitance of 2147 F g-1 at a discharge current of 1 A g-1 and outstanding cycling stability (99.5% capacitance retained after 2000 cycles), suggesting its potential application as an efficient electrode material for high-performance electrochemical capacitors. © 2014 Elsevier B.V.

Mondal, AK, Su, D, Wang, Y, Chen, S, Liu, Q & Wang, G 2014, 'Microwave hydrothermal synthesis of urchin-like NiO nanospheres as electrode materials for lithium-ion batteries and supercapacitors with enhanced electrochemical performances', JOURNAL OF ALLOYS AND COMPOUNDS, vol. 582, no. 1, pp. 522-527.
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Urchin-like NiO nanospheres were synthesised by a microwave hydrothermal method. The as-synthesised NiO nanospheres were characterised by X-ray diffraction, field emission scanning electron microscopy and transmission electron microscopy. It was found that NiO nanosphere consists of a nanoporous structure and nanosize crystals. When applied as anode materials in lithium-ion batteries, NiO nanospheres exhibited a high reversible specific capacity of 1027 mA h g-1, an excellent cycling performance and a good high rate capability. NiO nanospheres also showed a high specific capacitance as electrode materials for supercapacitors. © 2013 Elsevier B.V. All rights reserved.

Mondal, AK, Wang, B, Su, D, Wang, Y, Chen, S, Zhang, X & Wang, G 2014, 'Graphene/MnO2 hybrid nanosheets as high performance electrode materials for supercapacitors', Materials Chemistry and Physics, vol. 143, no. 2, pp. 740-746.
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Graphene/MnO2 hybrid nanosheets were prepared by incorporating graphene and MnO2 nanosheets in ethylene glycol. Scanning electron microscopy and transmission electron microscopy analyses confirmed nanosheet morphology of the hybrid materials. Graphene/MnO2 hybrid nanosheets with different ratios were investigated as electrode materials for supercapacitors by cyclic voltammetry (CV) and galvanostatic charge-discharge in 1 M Na2SO4 electrolyte. We found that the graphene/MnO2 hybrid nanosheets with a weight ratio of 1:4 (graphene:MnO2) delivered the highest specific capacitance of 320 F g-1. Graphene/MnO2 hybrid nanosheets also exhibited good capacitance retention on 2000 cycles. © 2013 Elsevier B.V. All rights reserved.

Moradi, A, Zhand, S, Ghaemi, A, Javid, N, Bazouri, M & Tabarraei, A 2014, 'Mutations in pre-core and basal-core promoter regions of hepatitis B virus in chronic HBV patients from Golestan, Iran.', Iran J Basic Med Sci, vol. 17, no. 5, pp. 370-377.
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OBJECTIVES: It has been reported that the mutation of the pre-core (PC) and basal-core promoter (BCP) may play an important role in the development of HBV-related hepatocellular carcinoma (HCC). In this study the PC and BCP mutations were investigated in chronic HBV patients. MATERIALS AND METHODS: In this study, 120 chronic HBV patients from Golestan, Northeast of Iran who were not vaccinated against HBV, were recruited from the year 2008 to 2012. HBV-DNA extraction from plasma and PCR were performed and positive PCR products were subjected to automated sequencing. RESULTS: One hundred out of 120 (83.3%) patients were HBeAg negative. Comparison of our nucleotide sequences with reference sequence showed high rate mutation in BCP and PC region (96.66%). Frame shift mutation was found in 78 (65%) of patients in BCP region, among them 8 (6.6%) patients showed mutation in PC region. CONCLUSION: Our results demonstrated high rate of mutations in BCP and PC regions among HBV chronic patients in Northeast of Iran.

Moran, MS, Ponce-Campos, GE, Huete, A, McClaran, MP, Zhang, Y, Hamerlynck, EP, Augustine, DJ, Gunter, SA, Kitchen, SG, Peters, DPC, Starks, PJ & Hernandez, M 2014, 'Functional response of U.S. grasslands to the early 21st-century drought', ECOLOGY, vol. 95, no. 8, pp. 2121-2133.
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Grasslands across the United States play a key role in regional livelihood and national food security. Yet, it is still unclear how this important resource will respond to the prolonged warm droughts and more intense rainfall events predicted with climate change. The early 21st-century drought in the southwestern United States resulted in hydroclimatic conditions that are similar to those expected with future climate change. We investigated the impact of the early 21st-century drought on aboveground net primary production (ANPP) of six desert and plains grasslands dominated by C4 (warm season) grasses in terms of significant deviations between observed and expected ANPP. In desert grasslands, drought-induced grass mortality led to shifts in the functional response to annual total precipitation (PT), and in some cases, new species assemblages occurred that included invasive species. In contrast, the ANPP in plains grasslands exhibited a strong linear function of the current-year PT and the previous-year ANPP, despite prolonged warm drought. We used these results to disentangle the impacts of interannual total precipitation, intra-annual precipitation patterns, and grassland abundance on ANPP, and thus generalize the functional response of C4 grasslands to predicted climate change. This will allow managers to plan for predictable shifts in resources associated with climate change related to fire risk, loss of forage, and ecosystem services. © 2014 by the Ecological Society of America.

Morelato, M, Baechler, S, Ribaux, O, Beavis, A, Tahtouh, M, Kirkbride, P, Roux, C & Margot, P 2014, 'Forensic intelligence framework-Part I: Induction of a transversal model by comparing illicit drugs and false identity documents monitoring', FORENSIC SCIENCE INTERNATIONAL, vol. 236, pp. 181-190.
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Forensic intelligence is a distinct dimension of forensic science. Forensic intelligence processes have mostly been developed to address either a specific type of trace or a specific problem. Even though these empirical developments have led to successes, they are trace-specific in nature and contribute to the generation of silos which hamper the establishment of a more general and transversal model. Forensic intelligence has shown some important perspectives but more general developments are required to address persistent challenges. This will ensure the progress of the discipline as well as its widespread implementation in the future. This paper demonstrates that the description of forensic intelligence processes, their architectures, and the methods for building them can, at a certain level, be abstracted from the type of traces considered. A comparative analysis is made between two forensic intelligence approaches developed independently in Australia and in Europe regarding the monitoring of apparently very different kind of problems: illicit drugs and false identity documents. An inductive effort is pursued to identify similarities and to outline a general model. Besides breaking barriers between apparently separate fields of study in forensic science and intelligence, this transversal model would assist in defining forensic intelligence, its role and place in policing, and in identifying its contributions and limitations. The model will facilitate the paradigm shift from the current case-by-case reactive attitude towards a proactive approach by serving as a guideline for the use of forensic case data in an intelligence-led perspective. A follow-up article will specifically address issues related to comparison processes, decision points and organisational issues regarding forensic intelligence (part II). © 2014 Elsevier Ireland Ltd.

Morelato, M, Beavis, A, Tahtouh, M, Ribaux, O, Kirkbride, P & Roux, C 2014, 'The use of organic and inorganic impurities found in MDMA police seizures in a drug intelligence perspective', SCIENCE & JUSTICE, vol. 54, no. 1, pp. 32-41.
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Traditional forensic drug profiling involves numerous analytical techniques, and the whole process is typically costly and may be time consuming. The aim of this study was to investigate the possibility of prioritising techniques utilised at the Australian Federal Police (AFP) for the chemical profiling of 3,4-methylenedioxymethylamphetamine (MDMA). The outcome would provide the AFP with the ability to obtain more timely and valuable results that could be used in an intelligence perspective. Correlation coefficients were used to obtain a similarity degree between a population of linked samples (within seizures) and a population of unlinked samples (between different seizures) and discrimination between the two populations was ultimately achieved. The results showed that gas chromatography-mass spectrometry (GC-MS) was well suited as a single technique to detect links between seizures and could be used in priority for operational intelligence purposes. Furthermore, the method was applied to seizures known or suspected (through their case information) to be linked to each other to assess the chemical similarity between samples. It was found that half of the seizures previously linked by the case number were also linked by the chemical profile. This procedure was also able to highlight links between cases that were previously unsuspected and retrospectively confirmed by circumstantial information. The findings are finally discussed in the broader forensic intelligence context, with a focus on how they could be successfully incorporated into investigations and in an intelligence-led policing perspective in order to understand trafficking markets. © 2014 Forensic Science Society.

Morton, JK & Gladstone, W 2014, 'Changes in rocky reef fish assemblages throughout an estuary with a restricted inlet', Hydrobiologia, vol. 724, no. 1, pp. 235-253.
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Rocky reef habitat is common in many estuaries, yet its role as a habitat for fishes is poorly understood. There is also limited understanding of how access of coastal species into estuaries and habitat quality can affect the distribution of rocky reef fishes within estuaries. This study used baited remote underwater video stations to determine spatial patterns in fish assemblages associated with rocky reef habitat throughout a barrier estuary with a permanently open but restricted inlet. Estuarine rocky reefs provided habitat for a diverse assemblage of fishes, many of which were large juveniles and subadults. In the absence of a pronounced salinity or temperature gradient, a clear transition in fish assemblages occurred from coastal waters, through the inlet channel, to the central estuary, and into the inner estuary. The inlet channel, notably its narrowness and length, limits tidal input into this estuary, which acts as a significant impediment to the dispersal of many coastal fishes, and insufficient habitat excludes many coastal rocky reef species from the inner estuary. This study highlights the need to recognise estuarine rocky reefs as providing habitat for diverse fish assemblages and the role inlets play in restricting access of coastal species.

Mozaner Bordin, DC, Alves, MNR, Cabrices, OG, de Campos, EG & De Martinis, BS 2014, 'A Rapid Assay for the Simultaneous Determination of Nicotine, Cocaine and Metabolites in Meconium Using Disposable Pipette Extraction and Gas Chromatography–Mass Spectrometry (GC–MS)', Journal of Analytical Toxicology, vol. 38, no. 1, pp. 31-38.
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Mullany, C, Keller, PA, Nugraha, AS & Wallman, JF 2014, 'Effects of methamphetamine and its primary human metabolite, p-hydroxymethamphetamine, on the development of the Australian blowfly Calliphora stygia', Forensic Science International, vol. 241, pp. 102-111.
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Murray, M, Dyari, HRE, Allison, SE & Rawling, T 2014, 'Lipid analogues as potential drugs for the regulation of mitochondrial cell death', British Journal of Pharmacology, vol. 171, no. 8, pp. 2051-2066.
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The mitochondrion plays an important role in the production of energy as ATP, the regulation of cell viability and apoptosis, and the biosynthesis of major structural and regulatory molecules, such as lipids. During ATP production, reactive oxygen species are generated that alter the intracellular redox state and activate apoptosis. Mitochondrial dysfunction is a well‐recognized component of the pathogenesis of diseases such as cancer. Understanding mitochondrial function, and how this is dysregulated in disease, offers the opportunity for the development of drug molecules to specifically target such defects. Altered energy metabolism in cancer, in which ATP production occurs largely by glycolysis, rather than by oxidative phosphorylation, is attributable in part to the up‐regulation of cell survival signalling cascades. These pathways also regulate the balance between pro‐ and anti‐apoptotic factors that may determine the rate of cell death and proliferation. A number of anti‐cancer drugs have been developed that target these factors and one of the most promising groups of agents in this regard are the lipid‐based molecules that act directly or indirectly at the mitochondrion. These molecules have emerged in part from an understanding of the mitochondrial actions of naturally occurring fatty acids. Some of these agents have already entered clinical trials because they specifically target known mitochondrial defects in the cancer cell.Linked ArticlesThis article is part of a themed issue on Mitochondrial Pharmacology: Energy, Injury & Beyond. To view the other articles in this issue visit HARMFUL ALGAE, vol. 39, pp. 242-252.
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Here the occurrence of the species Gambierdiscus yasumotoi is reported for the first time along a latitudinal gradient spanning more than 1550 km of the Australian Great Barrier Reef (GBR), a region with endemic ciguatera fish poisoning. G. yasumotoi was found at three tropical and sub tropical coral reef sites, Raine Island (northern GBR), Nelly Bay (central GBR) and Heron Island (southern GBR), indicating a wide-ranging distribution in tropical and subtropical eastern Australia. Specimens from Australia broadly fitted the original description of G. yasumotoi, but differed in some aspects, showing some similarities to Gambierdiscus ruetzleri. Molecular phylogenetic analyses based on nuclear rRNA gene sequences and morphological analyses showed specimens to be intermediate between the two species G. yasumotoi and G. ruetzleri. The full intraspecific diversity of these two species appears to be incompletely known, and these two species may represent a species complex. Strains of this species from other sites around the world have been found to produce an as yet unknown toxin, possibly an analogue of maitotoxin.

Murray, SA, Hoppenrath, M, Orr, RJS, Bolch, C, John, U, Diwan, R, Yauwenas, R, Harwood, T, de Salas, M, Neilan, B & Hallegraeff, G 2014, 'Alexandrium diversaporum sp. nov., a new non-saxitoxin producing species: Phylogeny, morphology and sxtA genes', HARMFUL ALGAE, vol. 31, pp. 54-65.
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Species of the PST producing planktonic marine dinoflagellate genus Alexandrium have been intensively scrutinised, and it is therefore surprising that new taxa can still be found. Here we report a new species, Alexandrium diversaporum nov. sp., isolated from spherical cysts found at two sites in Tasmania, Australia. This species differs in its morphology from all previously reported Alexandrium species, possessing a unique combination of morphological features: the presence of 2 size classes of thecal pores on the cell surface, a medium cell size, the size and shape of the 6″, 1', 2″″ and Sp plates, the lack of a ventral pore, a lack of anterior and posterior connecting pores, and a lack of chain formation. We determined the relationship of the two strains to other species of Alexandrium based on an alignment of concatenated SSU-ITS1, 5.8S, ITS2 and partial LSU ribosomal RNA sequences, and found A. diversaporum to be a sister group to Alexandrium leei with high support. A. leei shares several morphological features, including the relative size and shapes of the 6″, 1', 2″″ and Sp plates and the fact that some strains of A. leei have two size classes of thecal pores. We examined A. diversaporum strains for saxitoxin production and found them to be non-toxic. The species lacked sequences for the domain A4 of sxtA, as has been previously found for non-saxitoxin producing species of Alexandrium. © 2013 Elsevier B.V.

Naik, GV, Saha, B, Liu, J, Saber, SM, Stach, EA, Irudayaraj, JMK, Sands, TD, Shalaev, VM & Boltasseva, A 2014, 'Epitaxial superlattices with titanium nitride as a plasmonic component for optical hyperbolic metamaterials', Proceedings of the National Academy of Sciences, vol. 111, no. 21, pp. 7546-7551.
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Significance Plasmonic and metamaterial devices require high-performance material building blocks, both plasmonic and dielectric, to be useful in any real-world application. Here, we develop both plasmonic and dielectric materials that can be grown epitaxially into ultrathin and ultrasmooth layers with sharp interfaces. We show that a superlattice consisting of titanium nitride as a plasmonic component behaves as an optical hyperbolic metamaterial and exhibits extremely high photonic density of states.

NAWAZ, M, IQBAL, N, IDREES, S & ULLAH, I 2014, 'DREB1A from Oryza sativa var. IR6: homology modelling and molecular docking', TURKISH JOURNAL OF BOTANY, vol. 38, pp. 1095-1102.
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Nawaz, R, Asif, H, Khan, A, Ishtiaq, H, Shad, F & Siddiqui, S 2014, 'Drugs Targeting SNPrs35753505 of the NRG1 Gene May Prevent the Association of Neurological Disorder Schizophrenia in a Pakistani Population', CNS & Neurological Disorders - Drug Targets, vol. 13, no. 9, pp. 1604-1614.
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The Neuregulin 1 (NRG1) gene has been associated with schizophrenia in several populations, and all four types of NRG1 genes are linked with neurotransmitters activities. In this study for the first time we have demonstrated an association between NRG1 mutation and schizophrenia in Pakistani population. We examined the relationship of three genetic variants SNPs: rs3924999, rs2954041 and rs35753505 of NRG1 gene with the onset of disease. Genomic DNA samples were obtained from the blood of 100 patients and 80 matched controls. All three NRG1 SNPs were genotyped by polymerase chain reaction-restriction fragment length polymorphism method and further confirmed by DNA sequencing. The SNPs frequencies were estimated by Hardy-Weinberg equilibrium and Chi-square tests. Our study established a significant association of rs35753505 with schizophrenia but no association with rs3924999 and rs2954041. The frequency of risk allele C was significantly higher (62.5%) in rs35753505 patients when compared to controls (28.13%). Genotype frequency by Hardy-Weinberg equilibrium for SNPrs3924999 in patients was GG 77.4%, GA 21.12% and AA 1.44% and showed no association with the disease. Similarly, no genotype association was observed in rs2954041: GG 92.98%, GT 6.89%, TT 0.13% of NRG1. However, one unexpected G allele, 100% guanine (G) with no adenine (A) was found to be present in SNP rs35753505 in both patients and controls. This is an interesting finding that both cohorts display only allele G peak but no peak for allele A in the electropherogram for this SNP. Our results suggest that SNP rs35753505 of NRG1 plays an important role in conferring susceptibility to the schizophrenia in a Pakistani population.

Nawaz, R, Zahir, E, Siddiqui, S, Usmani, A & Shad, KF 2014, 'The Role of Trace Metals and Environmental Factors in the Onset and Progression of Schizophrenia in Pakistani Population', World Journal of Neuroscience, vol. 04, no. 05, pp. 450-460.
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Nelson, M, Roffey, P, McNevin, D, Lennard, C & Gahan, ME 2014, 'An overview of biosecurity in Australia', Australian Journal of Forensic Sciences, vol. 46, no. 4, pp. 383-396.
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Neville, SE, Ormerod, JT & Wand, MP 2014, 'Mean field variational Bayes for continuous sparse signal shrinkage: Pitfalls and remedies', Electronic Journal of Statistics, vol. 8, no. 1, pp. 1113-1151.
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© 2014, Institute of Mathematical Statistics. All rights received. We investigate mean field variational approximate Bayesian inference for models that use continuous distributions, Horseshoe, Negative-Exponential-Gamma and Generalized Double Pareto, for sparse signal shrinkage. Our principal finding is that the most natural, and simplest, mean field variational Bayes algorithm can perform quite poorly due to posterior dependence among auxiliary variables. More sophisticated algorithms, based on special functions, are shown to be superior. Continued fraction approximations via Lentz's Algorithm are developed to make the algorithms practical.

Nield, BS, Guzowski, R, Nassif, N, Simpson, AM & Martiniello-Wilks, R 2014, 'First use of Re: View: A tool to combine assessment tasks, marking criteria and graduate attributes for biochemistry students', International Journal of Innovation in Science and Mathematics Education, vol. 22, no. 7, pp. 49-64.
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In order to improve clarity of the link between assessment tasks and graduate attributes to students, Re:View was introduced across three undergraduate biochemistry subjects. Re:View is an online assessment tool which provides a direct visual link between graduate attributes and marking criteria. It also provides students with an easy access portal to retrieve their grade and assessor feedback on assessment tasks. Our aim was to improve the second and third year biochemistry student laboratory-based learning experience by developing and clarifying the link between assessment tasks, marking criteria and graduate attributes, using Re:View as the assessment tool. Student opinion showed Re:View was of benefit to align marking criteria with graduate attributes, and provided easy access to feedback which could be used to improve future work. This first use of Re:View, with development of criterion-referenced marking criteria and rubrics, has revolutionised assessment in the three biochemistry subjects under study. With the use of Re:View we have clarified the link between assessment tasks and marking criteria, and enhanced student engagement with laboratory-based assessment tasks, which has improved their written assessment performance.

Novikov, A & Shiryaev, AN 2014, 'Discussion on “Sequential Estimation for Time Series Models” by T. N. Sriram and Ross Iaci', Sequential Analysis, vol. 33, no. 2, pp. 182-185.
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We are glad to offer some comments on the invited paper of Professors Sriram and Iaci. These comments taken in the light of the paper under discussion will hopefully broaden the scope of future research in this important field. © 2014 Copyright Taylor & Francis Group, LLC.

Novikov, A, Kordzakhia, N & Ling, T 2014, 'On moments of Pitman estimators: the case of fractional Brownian Motion', Theory of Probability and its Applications, vol. 58, no. 4, pp. 601-614.
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In some non-regular statistical estimation problems, the limiting likelihoodprocesses are functionals of fractional Brownian motion (fBm) with Hurst'sparameter H; 0 < H <=? 1. In this paper we present several analytical andnumerical results on the moments of Pitman estimators represented in the formof integral functionals of fBm. We also provide Monte Carlo simulation resultsfor variances of Pitman and asymptotic maximum likelihood estimators.

Novikov, AA & Kordzakhia, NE 2014, 'Lower and upper bounds for prices of Asian-type options', Proceedings of the Steklov Institute of Mathematics, vol. 287, no. 1, pp. 225-231.
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© 2014, Pleiades Publishing, Ltd. In the context of dealing with financial risk management problems, it is desirable to have accurate bounds for option prices in situations when pricing formulae do not exist in the closed form. A unified approach for obtaining upper and lower bounds for Asian-type options is proposed in this paper. The bounds obtained are applicable to the continuous- and discrete-time frameworks for the case of time-dependent interest rates. Numerical examples are provided to illustrate the accuracy of the bounds.

Obata, K & Huete, AR 2014, 'Scaling effects on area-averaged fraction of vegetation cover derived using a linear mixture model with two-band spectral vegetation index constraints', JOURNAL OF APPLIED REMOTE SENSING, vol. 8, no. 1.
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This study investigated the mechanisms underlying the scaling effects that apply to a fraction of vegetation cover (FVC) estimates derived using two-band spectral vegetation index (VI) isoline-based linear mixture models (VI isoline-based LMM). The VIs included the normalized difference vegetation index, a soil-adjusted vegetation index, and a two-band enhanced vegetation index (EVI2). This study focused in part on the monotonicity of an area-averaged FVC estimate as a function of spatial resolution. The proof of monotonicity yielded measures of the intrinsic area-averaged FVC uncertainties due to scaling effects. The derived results demonstrate that a factor ξ, which was defined as a function of 'true' and 'estimated' endmember spectra of the vegetated and nonvegetated surfaces, was responsible for conveying monotonicity or nonmonotonicity. The monotonic FVC values displayed a uniform increasing or decreasing trend that was independent of the choice of the two-band VI. Conditions under which scaling effects were eliminated from the FVC were identified. Numerical simulations verifying the monotonicity and the practical utility of the scaling theory were evaluated using numerical experiments applied to Landsat7-Enhanced Thematic Mapper Plus (ETM+) data. The findings contribute to developing scale-invariant FVC estimation algorithms for multisensor and data continuity. © 2014 Society of Photo-Optical Instrumentation Engineers.

Oliver, BGG, Robinson, P, Peters, M & Black, J 2014, 'Viral infections and asthma: an inflammatory interface?', European Respiratory Journal, vol. 44, no. 6, pp. 1666-1681.
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Asthma is a chronic inflammatory disease of the airways in which the majority of patients respond to treatment with corticosteroids and β2-adrenoceptor agonists. Acute exacerbations of asthma substantially contribute to disease morbidity, mortality and healthcare costs, and are not restricted to patients who are not compliant with their treatment regimens. Given that respiratory viral infections are the principal cause of asthma exacerbations, this review article will explore the relationship between viral infections and asthma, and will put forward hypotheses as to why virus-induced exacerbations occur. Potential mechanisms that may explain why current therapeutics do not fully inhibit virus-induced exacerbations, for example, β2-adrenergic desensitisation and corticosteroid insensitivity, are explored, as well as which aspects of virus-induced inflammation are likely to be attenuated by current therapy.

Olivier, J, Wang, J & Grzebieta, R 2014, 'A systematic review of methods used to assess mandatory bicycle helmet legislation in New Zealand', Journal of the Australasian College of Road Safety, vol. 25, no. 4, pp. 24-31.
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Background: Mandatory helmet legislation (MHL)for cyclists became effective in New Zealand (NZ) on1 January 1994. Assessments of the NZ MHL have ledto conflicting conclusions regarding its effectiveness atreducing cycling head injury and risk of fatality. Thesestudies also differ in their use of analytic approaches anddata sources.Objectives: The aim of this paper is to systematicallyreview all studies that assess the NZ MHL in accordancewith quality criteria for assessing population-basedinterventions.Data Sources: A search of Medline, Scopus and Webof Science for peer-reviewed articles from 1994 to 9September 2014 was conducted.Study Selection: Documents were independently extractedby two reviewers and limited to original articles in peerreviewedjournals that assessed the NZ MHL in terms ofcycling head injury.Results: The results from three of the four included studiesindicated a positive effect of MHL for increasing helmetwearing and reducing head injuries. However, the findingsof these studies must be interpreted within the context ofmethodological limitations.Conclusion: We believe more high quality evaluations areneeded to provide evidence for an objective assessment ofMHL in NZ.

Olivier, J, Wang, J, Walter, S & Grzebieta, R 2014, 'Anti-Helmet Arguments: Lies, Damned Lies and Flawed Statistics', Journal of the Australasian College of Road Safety, vol. 25, no. 4, pp. 10-23.
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Bicycle helmets are designed to mitigate head injury duringa collision. In the early 1990’s, Australia and New Zealandmandated helmet wearing for cyclists in an effort toincrease helmet usage. Since that time, helmets and helmetlaws have been portrayed as a failure in the peer-reviewedliterature, by the media and various advocacy groups. Manyof these criticisms claim helmets are ineffective, helmetlaws deter cycling, helmet wearing increases the risk of anaccident, no evidence helmet laws reduce head injuries ata population level, and helmet laws result in a net healthreduction. This paper reviews the data and methods usedto support these arguments and shows they are statisticallyflawed. When the majority of evidence against helmets ormandatory helmet legislation (MHL) is carefully scrutinisedit appears overstated, misleading or invalid. Moreover,much of the statistical analysis has been conducted bypeople with known affiliations with anti-helmet or antiMHLorganisations.

Olson, SH, Parmley, J, Soos, C, Gilbert, M, Latorre-Margalef, N, Hall, JS, Hansbro, PM, Leighton, F, Munster, V & Joly, D 2014, 'Sampling Strategies and Biodiversity of Influenza A Subtypes in Wild Birds', PLoS ONE, vol. 9, no. 3, pp. e90826-e90826.
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Wild aquatic birds are recognized as the natural reservoir of avian influenza A viruses (AIV), but across high and low pathogenic AIV strains, scientists have yet to rigorously identify most competent hosts for the various subtypes. We examined 11,870 GenBank records to provide a baseline inventory and insight into patterns of global AIV subtype diversity and richness. Further, we conducted an extensive literature review and communicated directly with scientists to accumulate data from 50 non-overlapping studies and over 250,000 birds to assess the status of historic sampling effort. We then built virus subtype sample-based accumulation curves to better estimate sample size targets that capture a specific percentage of virus subtype richness at seven sampling locations. Our study identifies a sampling methodology that will detect an estimated 75% of circulating virus subtypes from a targeted bird population and outlines future surveillance and research priorities that are needed to explore the influence of host and virus biodiversity on emergence and transmission.

O'Reilly, M, Hansbro, PM, Horvat, JC, Beckett, EL, Harding, R & Sozo, F 2014, 'Bronchiolar Remodeling in Adult Mice Following Neonatal Exposure to Hyperoxia: Relation to Growth', The Anatomical Record, vol. 297, no. 4, pp. 758-769.
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ABSTRACTPreterm infants who receive supplemental oxygen for prolonged periods are at increased risk of impaired lung function later in life. This suggests that neonatal hyperoxia induces persistent changes in small conducting airways (bronchioles). Although the effects of neonatal hyperoxia on alveolarization are well documented, little is known about its effects on developing bronchioles. We hypothesized that neonatal hyperoxia would remodel the bronchiolar walls, contributing to altered lung function in adulthood. We studied three groups of mice (C57BL/6J) to postnatal day 56 (P56; adulthood) when they either underwent lung function testing or necropsy for histological analysis of the bronchiolar wall. One group inhaled 65% O2 from birth until P7, after which they breathed room air; this group experienced growth restriction (HE+GR group). We also used a group in which hyperoxia‐induced GR was prevented by dam rotation (HE group). A control group inhaled room air from birth. At P56, the bronchiolar epithelium of HE mice contained fewer Clara cells and more ciliated cells, and the bronchiolar wall contained ∼25% less collagen than controls; in HE+GR mice the bronchiolar walls had ∼13% more collagen than controls. Male HE and HE+GR mice had significantly thicker bronchiolar epithelium than control males and altered lung function (HE males: greater dynamic compliance; HE+GR males: lower dynamic compliance). We conclude that neonatal hyperoxia remodels the bronchiolar wall and, in adult males, affects lung function, but effects are altered by concomitant growth restriction. Our findings may partly explain the reports of poor lung function in ex‐preterm children and adults. Anat Rec, 297:758–769, 2014. © 2014 Wiley Periodicals, Inc.

Pai, S, Qin, J, Cavanagh, L, Mitchell, A, El-Assaad, F, Jain, R, Combes, V, Hunt, NH, Grau, GER & Weninger, W 2014, 'Real-Time Imaging Reveals the Dynamics of Leukocyte Behaviour during Experimental Cerebral Malaria Pathogenesis', PLoS Pathogens, vol. 10, no. 7, pp. e1004236-e1004236.
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During experimental cerebral malaria (ECM) mice develop a lethal neuropathological syndrome associated with microcirculatory dysfunction and intravascular leukocyte sequestration. The precise spatio-temporal context in which the intravascular immune response unfolds is incompletely understood. We developed a 2-photon intravital microscopy (2P-IVM)-based brain-imaging model to monitor the real-time behaviour of leukocytes directly within the brain vasculature during ECM. Ly6C(hi) monocytes, but not neutrophils, started to accumulate in the blood vessels of Plasmodium berghei ANKA (PbA)-infected MacGreen mice, in which myeloid cells express GFP, one to two days prior to the onset of the neurological signs (NS). A decrease in the rolling speed of monocytes, a measure of endothelial cell activation, was associated with progressive worsening of clinical symptoms. Adoptive transfer experiments with defined immune cell subsets in recombinase activating gene (RAG)-1-deficient mice showed that these changes were mediated by Plasmodium-specific CD8(+) T lymphocytes. A critical number of CD8(+) T effectors was required to induce disease and monocyte adherence to the vasculature. Depletion of monocytes at the onset of disease symptoms resulted in decreased lymphocyte accumulation, suggesting reciprocal effects of monocytes and T cells on their recruitment within the brain. Together, our studies define the real-time kinetics of leukocyte behaviour in the central nervous system during ECM, and reveal a significant role for Plasmodium-specific CD8(+) T lymphocytes in regulating vascular pathology in this disease.

Pandya‐Kumar, N, Shema, R, Kumar, M, Mayzlish‐Gati, E, Levy, D, Zemach, H, Belausov, E, Wininger, S, Abu‐Abied, M, Kapulnik, Y & Koltai, H 2014, 'Strigolactone analog GR24 triggers changes in PIN2 polarity, vesicle trafficking and actin filament architecture', New Phytologist, vol. 202, no. 4, pp. 1184-1196.
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SummaryStrigolactones (SLs) are plant hormones that regulate shoot and root development in a MAX2‐dependent manner. The mechanism underlying SLs' effects on roots is unclear.We used root hair elongation to measure root response to SLs. We examined the effects of GR24 (a synthetic, biologically active SL analog) on localization of the auxin efflux transporter PIN2, endosomal trafficking, and F‐actin architecture and dynamics in the plasma membrane (PM) of epidermal cells of the primary root elongation zone in wildtype (WT) Arabidopsis and the SL‐insensitive mutant max2. We also recorded the response to GR24 of trafficking (tir3), actin (der1) and PIN2 (eir1) mutants.GR24 increased polar localization of PIN2 in the PM of...

Pant, R, Marpaung, D, Kabakova, IV, Morrison, B, Poulton, CG & Eggleton, BJ 2014, 'On-chip stimulated Brillouin Scattering for microwave signal processing and generation', Laser & Photonics Reviews, vol. 8, no. 5, pp. 653-666.
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Park, J, Park, J-W, Han, J-H, Lee, S-W, Lee, K-Y, Ryu, H-S, Kim, K-W, Wang, G, Ahn, J-H & Ahn, H-J 2014, 'Charge–discharge properties of tin dioxide for sodium-ion battery', Materials Research Bulletin, vol. 58, pp. 186-189.
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Tin dioxide was investigated as an anode material for sodium-ion batteries. The Na/SnO2 cell delivered a first discharge capacity of 747 mAh/g, but the first charge capacity was 150 mAh/g. The irreversible capacity in the first cycle was examined through characterization by X-ray diffraction and scanning electron microscopy. X-ray diffraction analysis revealed that the SnO2 active material was not reduced fully to metallic Sn. Furrows and wrinkles were formed on the electrode surface owing to the volumetric expansion upon first discharge, which led to a deterioration of the electrode structure and a loss of electrical contact between the active materials. The analysis is summarized in the schematic drawing. © 2014 Elsevier Ltd. All rights reserved.

Parker, GK & Holt, SA 2014, 'Characterization of the Deposition ofn-Octanohydroxamate on Copper Surfaces', Journal of The Electrochemical Society, vol. 161, no. 5, pp. D277-D286.
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Patel, P, De Boer, L, Timms, P & Huston, WM 2014, 'Evidence of a conserved role for Chlamydia HtrA in the replication phase of the chlamydial developmental cycle', Microbes and Infection, vol. 16, no. 8, pp. 690-694.
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Identification of the HtrA inhibitor JO146 previously enabled us to demonstrate an essential function for HtrA during the mid-replicative phase of the Chlamydia trachomatis developmental cycle. Here we extend our investigations to other members of the Chlamydia genus. C. trachomatis isolates with distinct replicative phase growth kinetics showed significant loss of viable infectious progeny after HtrA was inhibited during the replicative phase. Mid-replicative phase addition of JO146 was also significantly detrimental to Chlamydia pecorum, Chlamydia suis and Chlamydia cavie. These data combined indicate that HtrA has a conserved critical role during the replicative phase of the chlamydial developmental cycle. © 2014 Institut Pasteur.

Patil, SS, Adetutu, EM, Aburto-Medina, A, Menz, IR & Ball, AS 2014, 'Biostimulation of indigenous communities for the successful dechlorination of tetrachloroethene (perchloroethylene)-contaminated groundwater', Biotechnology Letters, vol. 36, no. 1, pp. 75-83.
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Patil, SS, Adetutu, EM, Sheppard, PJ, Morrison, P, Menz, IR & Ball, AS 2014, 'Site-specific pre-evaluation of bioremediation technologies for chloroethene degradation', International Journal of Environmental Science and Technology, vol. 11, no. 7, pp. 1869-1880.
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Pearson, DJ, Webb, JK, Greenlees, MJ, Phillips, BL, Bedford, GS, Brown, GP, Thomas, J & Shine, R 2014, 'Behavioural responses of reptile predators to invasive cane toads in tropical Australia', AUSTRAL ECOLOGY, vol. 39, no. 4, pp. 448-454.
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The ecological impact of an invasive species can depend on the behavioural responses of native fauna to the invader. For example, the greatest risk posed by invasive cane toads (Rhinella marinaBufonidae) in tropical Australia is lethal poisoning of predators that attempt to eat a toad; and thus, a predator's response to a toad determines its vulnerability. We conducted standardized laboratory trials on recently captured (toad-naïve) predatory snakes and lizards, in advance of the toad invasion front as it progressed through tropical Australia. Responses to a live edible-sized toad differed strongly among squamate species. We recorded attacks (and hence, predator mortality) in scincid, agamid and varanid lizards, and in elapid, colubrid and pythonid snakes. Larger-bodied predators were at greater risk, and some groups (elapid snakes and varanid lizards) were especially vulnerable. However, feeding responses differed among species within families and within genera. Some taxa (notably, many scincid and agamid lizards) do not attack toads; and many colubrid snakes either do not consume toads, or are physiologically resistant to the toad's toxins. Intraspecific variation in responses means that even in taxa that apparently are unaffected by toad invasion at the population level, some individual predators nonetheless may be fatally poisoned by invasive cane toads. © 2013 Ecological Society of Australia.

Pendarvis, K, Padula, MP, Tacchi, JL, Petersen, AC, Djordjevic, SP, Burgess, SC & Minion, F 2014, 'Proteogenomic mapping of Mycoplasma hyopneumoniae virulent strain 232', BMC Genomics, vol. 15, no. 1, pp. 576-576.
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Background: Mycoplasma hyopneumoniae causes respiratory disease in swine and contributes to the porcine respiratory disease complex, a major disease problem in the swine industry. The M. hyopneumoniae strain 232 genome is one of the smallest and best annotated microbial genomes, containing only 728 annotated genes and 691 known proteins. Standard protein databases for mass spectrometry only allow for the identification of known and predicted proteins, which if incorrect can limit our understanding of the biological processes at work. Proteogenomic mapping is a methodology which allows the entire 6-frame genome translation of an organism to be used as a mass spectrometry database to help identify unknown proteins as well as correct and confirm existing annotations. This methodology will be employed to perform an in-depth analysis of the M. hyopneumoniae proteome.Results: Proteomic analysis indicates 483 of 691 (70%) known M. hyopneumoniae strain 232 proteins are expressed under the culture conditions given in this study. Furthermore, 171 of 328 (52%) hypothetical proteins have been confirmed. Proteogenomic mapping resulted in the identification of previously unannotated genes gatC and rpmF and 5-prime extensions to genes mhp063, mhp073, and mhp451, all conserved and annotated in other M. hyopneumoniae strains and Mycoplasma species. Gene prediction with Prodigal, a prokaryotic gene predicting program, completely supports the new genomic coordinates calculated using proteogenomic mapping.Conclusions: Proteogenomic mapping showed that the protein coding genes of the M. hyopneumoniae strain 232 identified in this study are well annotated. Only 1.8% of mapped peptides did not correspond to genes defined by the current genome annotation. This study also illustrates how proteogenomic mapping can be an important tool to help confirm, correct and append known gene models when using a genome sequence as search space for peptide mass spectra. Using a gene predicti...

Pernice, M & Levy, O 2014, 'Novel tools integrating metabolic and gene function to study the impact of the environment on coral symbiosis', Frontiers in Microbiology, vol. 5, pp. 1-6.
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The symbiotic dinoflagellates (genus Symbiodinium) inhabiting coral endodermal tissues are well known for their role as keystone symbiotic partners, providing corals with enormous amounts of energy acquired via photosynthesis and the absorption of dissolved nutrients. In the past few decades, corals reefs worldwide have been increasingly affected by coral bleaching (i.e., the breakdown of the symbiosis between corals and their dinoflagellate symbionts), which carries important socio-economic implications. Consequently, the number of studies focusing on the molecular and cellular processes underlying this biological phenomenon has grown rapidly, and symbiosis is now widely recognized as a major topic in coral biology. However, obtaining a clear image of the interplay between the environment and this mutualistic symbiosis remains challenging. Here, we review the potential of recent technological advances in molecular biology and approaches using stable isotopes to fill critical knowledge gaps regarding coral symbiotic function. Finally, we emphasize that the largest opportunity to achieve the full potential in this field arises from the integration of these technological advances.

Pernice, M, Simpson, SJ & Ponton, F 2014, 'Towards an integrated understanding of gut microbiota using insects as model systems', Journal of Insect Physiology, vol. 69, pp. 12-18.
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Metazoans form symbioses with microorganisms that synthesize essential nutritional compounds and increase their efficiency to digest and absorb nutrients. Despite the growing awareness that microbes within the gut play key roles in metabolism, health and development of metazoans, symbiotic relationships within the gut are far from fully understood. Insects, which generally harbor a lower microbial diversity than vertebrates, have recently emerged as potential model systems to study these interactions. In this review, we give a brief overview of the characteristics of the gut microbiota in insects in terms of low diversity but high variability at intra- and interspecific levels and we investigate some of the ecological and methodological factors that might explain such variability. We then emphasize how studies integrating an array of techniques and disciplines have the potential to provide new understanding of the biology of this micro eco-system.

Pesenti, A, Taudte, RV, McCord, B, Doble, P, Roux, C & Blanes, L 2014, 'Coupling Paper-Based Microfluidics and Lab on a Chip Technologies for Confirmatory Analysis of Trinitro Aromatic Explosives', ANALYTICAL CHEMISTRY, vol. 86, no. 10, pp. 4707-4714.
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A new microfluidic paper-based analytical device (μPAD) in conjunction with confirmation by a lab on chip analysis was developed for detection of three trinitro aromatic explosives. Potassium hydroxide was deposited on the μPADs (0.5 μL, 1.5 M), creating a color change reaction when explosives are present, with detection limits of approximately 7.5 ± 1.0 ng for TNB, 12.5 ± 2.0 ng for TNT and 15.0 ± 2.0 ng for tetryl. For confirmatory analysis, positive μPADs were sampled using a 5 mm hole-punch, followed by extraction of explosives from the punched chad in 30 s using 20 μL borate/SDS buffer. The extractions had efficiencies of 96.5 ± 1.7%. The extracted explosives were then analyzed with the Agilent 2100 Bioanalyzer lab on a chip device with minimum detectable amounts of 3.8 ± 0.1 ng for TNB, 7.0 ± 0.9 ng for TNT, and 4.7 ± 0.2 ng for tetryl. A simulated in-field scenario demonstrated the feasibility of coupling the μPAD technique with the lab on a chip device to detect and identify 1 μg of explosives distributed on a surface of 100 cm2. © 2014 American Chemical Society.

Petrou, K, Belgio, E & Ruban, AV 2014, 'pH sensitivity of chlorophyll fluorescence quenching is determined by the detergent/protein ratio and the state of LHCII aggregation', BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS, vol. 1837, no. 9, pp. 1533-1539.
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Here we show how the protein environment in terms of detergent concentration/protein aggregation state, affects the sensitivity to pH of isolated, native LHCII, in terms of chlorophyll fluorescence quenching. Three detergent concentrations (200, 20 and 6 μM n-dodecyl β-d-maltoside) have been tested. It was found that at the detergent concentration of 6 μM, low pH quenching of LHCII is close to the physiological response to lumen acidification possessing pK of 5.5. The analysis has been conducted both using arbitrary PAM fluorimetry measurements and chlorophyll fluorescence lifetime component analysis. The second led to the conclusion that the 3.5 ns component lifetime corresponds to an unnatural state of LHCII, induced by the detergent used for solubilising the protein, whilst the 2 ns component is rather the most representative lifetime component of the conformational state of LHCII in the natural thylakoid membrane environment when the non-photochemical quenching (NPQ) was absent. The 2 ns component is related to a pre-aggregated LHCII that makes it more sensitive to pH than the trimeric LHCII with the dominating 3.5 ns lifetime component. The pre-aggregated LHCII displayed both a faster response to protons and a shift in the pK for quenching to higher values, from 4.2 to 4.9. We concluded that environmental factors like lipids, zeaxanthin and PsbS protein that modulate NPQ in vivo could control the state of LHCII aggregation in the dark that makes it more or less sensitive to the lumen acidification. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: Keys to Produce Clean Energy. © 2013 Elsevier B.V.

Petrou, K, Trimborn, S, Kuehl, M & Ralph, PJ 2014, 'Desiccation stress in two intertidal beachrock biofilms', MARINE BIOLOGY, vol. 161, no. 8, pp. 1765-1773.
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Chlorophyll a fluorescence was used to look at the effect of desiccation on the photophysiology in two beachrock microbial biofilms from the intertidal rock platform of Heron Island, Australia. The photophysiological response to desiccation differed between the beachrock microbial communities. The black biofilm from the upper shoreline, dominated by Calothrix sp., showed a response typical of desiccation-tolerant cyanobacteria, where photosynthesis closed down during air exposure with a rapid and complete recovery upon rehydration. In contrast, the pink biofilm from the mid-intertidal zone, dominated by Blennothrix sp., showed no distinct response to desiccation stress and instead maintained reduced photosynthesis throughout drying and re-wetting cycles. Spatial differences in photosynthetic activity within the black biofilm were evident with a faster recovery rate of photosynthesis in the surface cyanobacteria than in the deeper layers of the biofilm. There was no variation with depth in the pink biofilm. The photophysiological differences in desiccation responses between the beachrock biofilms exemplify the ecological niche specialisation of these complex microbial communities, where the functional differences help to explain their vertical distribution on the intertidal shoreline.

Petrou, K, Trimborn, S, Rost, B, Ralph, PJ & Hassler, CS 2014, 'The impact of iron limitation on the physiology of the Antarctic diatom Chaetoceros simplex', MARINE BIOLOGY, vol. 161, no. 4, pp. 925-937.
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Iron availability strongly governs the growth of Southern Ocean phytoplankton. To investigate how iron limitation affects photosynthesis as well as the uptake of carbon and iron in the Antarctic diatom Chaetoceros simplex, a combination of chlorophyll a fluorescence measurements and radiotracer incubations in the presence and absence of chemical inhibitors was conducted. Iron limitation in C. simplex led to a decline in growth rates, photochemical efficiency and structural changes in photosystem II (PSII), including a reorganisation of photosynthetic units in PSII and an increase in size of the functional absorption cross section of PSII. Iron-limited cells further exhibited a reduced plastoquinone pool and decreased photosynthetic electron transport rate, while non-photochemical quenching and relative xanthophyll pigment content were strongly increased, suggesting a photoprotective response. Additionally, iron limitation resulted in a strong decline in carbon fixation and thus the particulate organic carbon quotas. Inhibitor studies demonstrated that, independent of the iron supply, carbon fixation was dependent on internal, but not on extracellular carbonic anhydrase activity. Orthovanadate more strongly inhibited iron uptake in iron-limited cells, indicating that P-type ATPase transporters are involved in iron uptake. The stronger reduction in iron uptake by ascorbate in iron-limited cells suggests that the re-oxidation of iron is required before it can be taken up and further supports the presence of a high-affinity iron transport pathway. The measured changes to photosystem architecture and shifts in carbon and iron uptake strategies in C. simplex as a result of iron limitation provide evidence for a complex interaction of these processes to balance the iron requirements for photosynthesis and carbon demand for sustained growth in iron-limited waters. © 2014 The Author(s).

Pillai, U, Phillips, K, Wilkins, G, Baxter, RC, Benn, DE, Parker, NR, Smith, RC & Marsh, DJ 2014, 'Factors that May Influence the Willingness of Cancer Patients to Consent for Biobanking', Biopreservation and Biobanking, vol. 12, no. 6, pp. 409-414.
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Pinart, M, Hussain, F, Shirali, S, Li, F, Zhu, J, Clark, AR, Ammit, AJ & Chung, KF 2014, 'Role of mitogen-activated protein kinase phosphatase-1 in corticosteroid insensitivity of chronic oxidant lung injury', European Journal of Pharmacology, vol. 744, pp. 108-114.
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Oxidative stress plays an important role in the pathogenesis of chronic obstructive pulmonary disease (COPD) and in the induction of corticosteroid (CS) insensitivity. Chronic ozone exposure leads to a model of COPD with lung inflammation and emphysema. Mitogen-activated protein kinase phosphatase-1 (MKP-1) may underlie CS insensitivity in COPD. We determined the role played by MKP-1 by studying the effect of corticosteroids in wild-type C57/BL6J and MKP-1(-/-) mice after chronic ozone exposure. Mice were exposed to ozone (3 ppm, 3 h) 12 times over 6 weeks. Dexamethasone (0.1 or 2 mg/kg; intraperitoneally) was administered before each exposure. Mice were studied 24 h after final exposure. In ozone-exposed C57/BL6J mice, bronchial hyperresponsiveness (BHR) was not inhibited by both doses of dexamethasone, but in MKP-1(-/-) mice, there was a small inhibition by high dose dexamethasone (2 mg/kg). There was an increase in mean linear intercept after chronic ozone exposure in both strains which was CS-insensitive. There was lesser inflammation after low dose of dexamethasone in MKP-1(-/-) mice compared to C57/Bl6J mice. Epithelial and collagen areas were modulated in ozone-exposed MKP-1(-/-) mice treated with dexamethasone compared to C57/Bl6J mice. MKP-1 regulated the expression of MMP-12, IL-13 and KC induced by ozone but did not alter dexamethasone׳s effects. Bronchial hyperresponsiveness, lung inflammation and emphySEMa after chronic exposure are CS-insensitive, and the contribution of MKP-1 to CS sensitivity in this model was negligible.

Pineda, SS, Sollod, BL, Wilson, D, Darling, A, Sunagar, K, Undheim, EAB, Kely, L, Antunes, A, Fry, BG & King, GF 2014, 'Diversification of a single ancestral gene into a successful toxin superfamily in highly venomous Australian funnel-web spiders', BMC Genomics, vol. 15, no. 1, pp. 1-16.
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Background Spiders have evolved pharmacologically complex venoms that serve to rapidly subdue prey and deter predators. The major toxic factors in most spider venoms are small, disulfide-rich peptides. While there is abundant evidence that snake venoms evolved by recruitment of genes encoding normal body proteins followed by extensive gene duplication accompanied by explosive structural and functional diversification, the evolutionary trajectory of spider-venom peptides is less clear. Results Here we present evidence of a spider-toxin superfamily encoding a high degree of sequence and functional diversity that has evolved via accelerated duplication and diversification of a single ancestral gene. The peptides within this toxin superfamily are translated as prepropeptides that are posttranslationally processed to yield the mature toxin. The N-terminal signal sequence, as well as the protease recognition site at the junction of the propeptide and mature toxin are conserved, whereas the remainder of the propeptide and mature toxin sequences are variable. All toxin transcripts within this superfamily exhibit a striking cysteine codon bias. We show that different pharmacological classes of toxins within this peptide superfamily evolved under different evolutionary selection pressures. Conclusions Overall, this study reinforces the hypothesis that spiders use a combinatorial peptide library strategy to evolve a complex cocktail of peptide toxins that target neuronal receptors and ion channels in prey and predators. We show that the ?-hexatoxins that target insect voltage-gated calcium channels evolved under the influence of positive Darwinian selection in an episodic fashion, whereas the ?-hexatoxins that target insect calcium-activated potassium channels appear to be under negative selection. A majority of the diversifying sites in the ?-hexatoxins are concentrated on the molecular surface of the toxins, thereby facilitating neofunctionalisation leading to new toxin...

Pokharel, D, Padula, MP, Lu, JF, Tacchi, JL, Luk, F, Djordjevic, SP & Bebawy, M 2014, 'Proteome analysis of multidrug‐resistant, breast cancer–derived microparticles', Journal of Extracellular Vesicles, vol. 3, no. 1, pp. 24384-24384.
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Cancer multidrug resistance (MDR) occurs when cancer cells evade the cytotoxic actions of chemotherapeutics through the active efflux of drugs from within the cells. Our group have previously demonstrated that multidrug‐resistant breast cancer cells spontaneously shed microparticles (MPs) and that these MPs can transfer resistance to drug‐responsive cells and confer MDR on those cells in as little as 4 h. Furthermore, we also showed that, unlike MPs derived from leukaemia cells, breast cancer–derived MPs display a tissue selectivity in the transfer of P‐glycoprotein (P‐gp), transferring the resistance protein only to malignant breast cells. This study aims to define the proteome of breast cancer–derived MPs in order to understand the differences in protein profiles between those shed from drug‐resistant versus drug‐sensitive breast cancer cells. In doing so, we detail the protein cargo required for the intercellular transfer of MDR to drug‐sensitive recipient cells and the factors governing the transfer selectivity to malignant breast cells. We describe the first proteomic analysis of MPs derived from human breast cancer cells using SDS PAGE and liquid chromatography–tandem mass spectrometry (LC/MS/MS), in which we identify 120 unique proteins found only in drug‐resistant, breast cancer–derived MPs. Our results demonstrate that the MP‐mediated transfer of P‐gp to recipient cells occurs alongside CD44; the Ezrin, Radixin and Moesin protein family (ERM); and cytoskeleton motor proteins within the MP cargo.

Poon, AH, Houseman, EA, Ryan, L, Sparrow, D, Vokonas, PS & Litonjua, AA 2014, 'Variants of Asthma and Chronic Obstructive Pulmonary Disease Genes and Lung Function Decline in Aging', JOURNALS OF GERONTOLOGY SERIES A-BIOLOGICAL SCIENCES AND MEDICAL SCIENCES, vol. 69, no. 7, pp. 907-913.
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Background. A substantial proportion of the general population has low lung function, and lung function is known to decrease as we age. Low lung function is a feature of several pulmonary disorders, such as uncontrolled asthma and chronic obstructive pulmonary disease. The objective of this study is to investigate the association of polymorphisms in asthma and chronic obstructive pulmonary disease candidate genes with rates of lung function decline in a general population sample of aging men. Methods. We analyzed data from a cohort of 1,047 Caucasian men without known lung disease, who had a mean of 25 years of lung function data, and on whom DNA was available. The cohort was randomly divided into two groups, and we tested a total of 940 single-nucleotide polymorphisms in 44 asthma and chronic obstructive pulmonary disease candidate genes in the first group (testing cohort, n = 545) for association with change in forced expiratory volume in 1 second over time. Results. One hundred nineteen single-nucleotide polymorphisms that showed nominal associations in the testing cohort were then genotyped and tested in the second group (replication cohort, n = 502). Evidence for association from the testing and replication cohorts were combined, and after adjustment for multiple testing, seven variants of three genes (DPP10, NPSR1, and ADAM33) remained significantly associated with change in forced expiratory volume in 1 second over time. Conclusions. Our findings that genetic variants of genes involved in asthma and chronic obstructive pulmonary disease are associated with lung function decline in normal aging participants suggest that similar genetic mechanisms may underlie lung function decline in both disease and normal aging processes. © The Author 2013.

Porto, SKSS, Nogueira, T, Blanes, L, Doble, P, Sabino, BD, do Lago, CL & Angnes, L 2014, 'Analysis of Ecstasy Tablets Using Capillary Electrophoresis with Capacitively Coupled Contactless Conductivity Detection', Journal of Forensic Sciences, vol. 59, no. 6, pp. 1622-1626.
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AbstractA method for the identification of 3,4‐methylenedioxymethamphetamine (MDMA) and meta‐chlorophenylpiperazine (mCPP) was developed employing capillary electrophoresis (CE) with capacitively coupled contactless conductivity detection (C4D). Sample extraction, separation, and detection of “Ecstasy” tablets were performed in <10 min without sample derivatization. The separation electrolyte was 20 mm TAPS/Lithium, pH 8.7. Average minimal detectable amounts for MDMA and mCPP were 0.04 mg/tablet, several orders of magnitude lower than the minimum amount encountered in a tablet. Seven different Ecstasy tablets seized in Rio de Janeiro, Brazil, were analyzed by CE‐C4D and compared against routine gas chromatography‐mass spectrometry (GC‐MS). The CE method demonstrated sufficient selectivity to discriminate the two target drugs, MDMA and mCPP, from the other drugs present in seizures, namely amphepramone, fenproporex, caffeine, lidocaine, and cocaine. Separation was performed in <90 sec. The advantages of using C

Poulton, AJ, Stinchcombe, MC, Achterberg, EP, Bakker, DCE, Dumousseaud, C, Lawson, HE, Lee, GA, Richier, S, Suggett, DJ & Young, JR 2014, 'Coccolithophores on the north-west European shelf: calcification rates and environmental controls', Biogeosciences, vol. 11, no. 14, pp. 3919-3940.
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Abstract. Coccolithophores are a key functional group in terms of the pelagic production of calcium carbonate (calcite), although their contribution to shelf sea biogeochemistry, and how this relates to environmental conditions, is poorly constrained. Measurements of calcite production (CP) and coccolithophore abundance were made on the north-west European shelf to examine trends in coccolithophore calcification along natural gradients of carbonate chemistry, macronutrient availability and plankton composition. Similar measurements were also made in three bioassay experiments where nutrient (nitrate, phosphate) and pCO2 levels were manipulated. Nanoflagellates (< 10 μm) dominated chlorophyll biomass and primary production (PP) at all but one sampling site, with CP ranging from 0.6 to 9.6 mmol C m−2 d−1. High CP and coccolithophore abundance occurred in a diatom bloom in fully mixed waters off Heligoland, but not in two distinct coccolithophore blooms in the central North Sea and Western English Channel. Coccolithophore abundance and CP showed no correlation with nutrient concentrations or ratios, while significant (p < 0.01) correlations between CP, cell-specific calcification (cell-CF) and irradiance in the water column highlighted how light availability exerts a strong control on pelagic CP. In the experimental bioassays, Emiliania-huxleyi-dominated coccolithophore communities in shelf waters (northern North Sea, Norwegian Trench) showed a strong response in terms of CP to combined nitrate and phosphate addition, mediated by changes in cell-CF and growth rates. In contrast, an offshore diverse coccolithophore community (Bay of Biscay) showed no response to nutrient addition, while light availability or mortality may have been more important in controlling this community. Sharp decreases in pH and a rough halving of calcite saturation states in the bioassay experiments led to decreased CP in the Bay of Biscay and northern North Sea, but n...

Poulton, AJ, Stinchcombe, MC, Achterberg, EP, Bakker, DCE, Dumousseaud, C, Lawson, HE, Lee, GA, Richier, S, Suggett, DJ & Young, JR 2014, 'Coccolithophores on the north-west European shelf: calcification rates and environmental controls', Biogeosciences Discussions, vol. 11, no. 2, pp. 2685-2733.
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Abstract. Coccolithophores are a key functional group in terms of the pelagic production of calcium carbonate (calcite), although their contribution to shelf-sea biogeochemistry, and how this relates to environmental conditions, is poorly constrained. Measurements of calcite production (CP) and coccolithophore abundance were made on the north-west European shelf to examine trends in coccolithophore calcification along natural gradients of carbonate chemistry, macronutrient availability and plankton composition. Similar measurements were also made in three bioassay experiments where nutrient (nitrate, phosphate) and pCO2 levels were manipulated. Nanoflagellates (< 10 μm) dominated chlorophyll biomass and primary production (PP) at all but one sampling site, with CP ranging from 0.6–9.6 mmol C m−2d−1. Highest CP and coccolithophore cell abundance occurred in a diatom bloom in fully mixed waters off Helgoland, rather than in two distinct coccolithophore blooms in the central North Sea and Western English Channel. Estimates of coccolithophore contributions to total PP and nanoplankton PP were generally < 5%, apart from in a coccolithophore bloom at the Western English Channel Observatory (E1) where coccolithophores contributed up to 11% and at Helgoland where they contributed ~23% to nanoplankton PP. Variability in CP was influenced by cell numbers, species composition and cell-normalised calcification rates under both in situ conditions and in the experimental bioassays. Water column structure and light availability had a strong influence on cellular calcification, whereas nitrate (N) to phosphate (P) ratios influenced bulk CP. Coccolithophore communities in the northern North Sea and over the Norwegian Trench showed responses to N and P addition whereas oceanic communities in the Bay of Biscay showed no response. Sharp decreases in pH and a rough halving of calcite saturation states in the bioassay experiments led to decreased CP in the Bay ...

Pradella, N, Fowler, AM, Booth, DJ & Macreadie, PI 2014, 'Fish assemblages associated with oil industry structures on the continental shelf of north-western Australia', JOURNAL OF FISH BIOLOGY, vol. 84, no. 1, pp. 247-255.
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This study provides the first assessment of fish associations with oil and gas structures located in deep water (85-175m) on Australia's north-west continental shelf, using rare oil industry video footage obtained from remotely operated vehicles. A diverse range of taxa were observed associating with the structures, including reef-dependent species and transient pelagic species. Ten commercially fished species were observed, the most abundant of which was Lutjanus argentimaculatus, with an estimated biomass for the two deepest structures (Goodwyn and Echo) of 109kg. © 2013 The Fisheries Society of the British Isles.

Prieto-García, A, Castells, MC, Hansbro, PM & Stevens, RL 2014, 'Mast Cell–Restricted Tetramer-Forming Tryptases and Their Beneficial Roles in Hemostasis and Blood Coagulation', Immunology and Allergy Clinics of North America, vol. 34, no. 2, pp. 263-281.
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Tetramer-forming tryptase (hTryptase-β) was recently discovered to have a prominent role in preventing the internal accumulation of life-threatening fibrin deposits and fibrin-platelet clots. The anticoagulant activity of hTryptase-β is an explanation for the presence of hemorrhagic disorders in some patients with anaphylaxis or mastocytosis. The fragments of hFibrinogen formed by the proteolysis of this prominent protein by hTryptase-β could be used as biomarkers in the blood and/or urine for the identification and monitoring of patients with mast cell-dependent disorders. Recombinant hTryptase-β has potential to be used in clinical settings where it is desirable to inhibit blood coagulation.

Quiroz, M, Kohn, R, Villani, M & Tran, M-N 2014, 'Speeding Up MCMC by Efficient Data Subsampling', JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION, vol. 114, no. 526, pp. 831-843.
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We propose Subsampling MCMC, a Markov Chain Monte Carlo (MCMC) frameworkwhere the likelihood function for $n$ observations is estimated from a randomsubset of $m$ observations. We introduce a highly efficient unbiased estimatorof the log-likelihood based on control variates, such that the computing costis much smaller than that of the full log-likelihood in standard MCMC. Thelikelihood estimate is bias-corrected and used in two dependent pseudo-marginalalgorithms to sample from a perturbed posterior, for which we derive theasymptotic error with respect to $n$ and $m$, respectively. We propose apractical estimator of the error and show that the error is negligible even fora very small $m$ in our applications. We demonstrate that Subsampling MCMC issubstantially more efficient than standard MCMC in terms of sampling efficiencyfor a given computational budget, and that it outperforms other subsamplingmethods for MCMC proposed in the literature.

Rahman, MA, Hogan, B, Duncan, E, Doyle, C, Krassoi, R, Rahman, MM, Naidu, R, Lim, RP, Maher, W & Hassler, C 2014, 'Toxicity of arsenic species to three freshwater organisms and biotransformation of inorganic arsenic by freshwater phytoplankton (Chlorella sp CE-35)', ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY, vol. 106, pp. 126-135.
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In the environment, arsenic (As) exists in a number of chemical species, and arsenite (AsIII) and arsenate (AsV) dominate in freshwater systems. Toxicity of As species to aquatic organisms is complicated by their interaction with chemicals in water such as phosphate that can influence the bioavailability and uptake of AsV. In the present study, the toxicities of AsIII, AsV and dimethylarsinic acid (DMA) to three freshwater organisms representing three phylogenetic groups: a phytoplankton (Chlorella sp. strain CE-35), a floating macrophyte (Lemna disperma) and a cladoceran grazer (Ceriodaphnia cf. dubia), were determined using acute and growth inhibition bioassays (EC50) at a range of total phosphate (TP) concentrations in OECD medium. The EC50 values of AsIII, AsV and DMA were 27±10, 1.15±0.04 and 19±3mg L-1 for Chlorella sp. CE-35; 0.57±0.16, 2.3±0.2 and 56±15mgL-1 for L. disperma, and 1.58±0.05, 1.72±0.01 and 5.9±0.1mgL-1 for C. cf. dubia, respectively. The results showed that AsIII was more toxic than AsV to L. disperma; however, AsV was more toxic than AsIII to Chlorella sp. CE-35. The toxicities of AsIII and AsV to C. cf. dubia were statistically similar (p>0.05). DMA was less toxic than iAs species to L. disperma and C. cf. dubia, but more toxic than AsIII to Chlorella sp. CE-35. The toxicity of AsV to Chlorella sp. CE-35 and L. disperma decreased with increasing TP concentrations in the growth medium. Phosphate concentrations did not influence the toxicity of AsIII to either organism. Chlorella sp. CE-35 showed the ability to reduce AsV to AsIII, indicating a substantial influence of phytoplankton on As biogeochemistry in freshwater aquatic systems. © 2014 Elsevier Inc.

Rahman, MA, Rahman, MM, Reichman, SM, Lim, RP & Naidu, R 2014, 'Arsenic Speciation in Australian-Grown and Imported Rice on Sale in Australia: Implications for Human Health Risk', Journal of Agricultural and Food Chemistry, vol. 62, no. 25, pp. 6016-6024.
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Rice is an important route of arsenic (As) exposure to humans, especially populations with rice-based diets. Human health risk of As varies greatly with rice variety and country of origin. The purpose of the present study was to determine total and speciated As in Australian-grown and imported rice on sale in Australia to assess their health risk to consumers. The total As (tAs) concentrations in Australian-grown organic brown, medium grain brown, and organic white rice were 438 ± 23, 287 ± 03, and 283 ± 18 μg kg-1 dry weight (d wt), respectively. In Bangladeshi, Indian, Pakistani, and Thai rice imported and on sale in Australia, tAs concentrations were 56 ± 05, 92 ± 10, 82 ± 06 and 172 ± 24 μg kg-1, respectively. Asian rice contained mainly inorganic As (iAs; 86-99%), whereas 18-26% of the tAs in Australian-grown rice was dimethylarsinic acid (DMA). Relatively higher concentrations of tAs in Australian-grown rice than that in imported rice of Asian origin suggest that Australian-grown rice may be a health risk for the consumers. It was estimated that Australian-grown organic brown rice can contribute up to 98% of the FAO/WHO recommended maximum tolerable daily intake limit of iAs (2.1 μg kg-1 body wt day -1) for Asian immigrants. However, other Australian consumers including European immigrants are unlikely to be at risk to As from rice diets due to their lower rice consumption rates than that of Asian immigrants. The risk assessment showed that imported rice on sale in Australia was likely to pose a lower health risk to consumers than Australian-grown rice. © 2014 American Chemical Society.

Rahman, MA, Rahman, MM, Reichman, SM, Lim, RP & Naidu, R 2014, 'Heavy metals in Australian grown and imported rice and vegetables on sale in Australia: Health hazard', ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY, vol. 100, pp. 53-60.
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Dietary exposure to heavy metals is a matter of concern for human health risk through the consumption of rice, vegetables and other major foodstuffs. In the present study, we investigated concentrations of cadmium (Cd), cobalt (Co), chromium (Cr), copper (Cu), manganese (Mn), nickel (Ni), lead (Pb), and zinc (Zn) in Australian grown and imported rice and vegetables on sale in Australia. The mean concentrations of Cd, Co, Cr, Cu, Mn, Ni, Pb, and Zn in Australian grown rice were 7.5 mg kg1, 21 mg kg1, 144 mg kg1, 2.9 mg kg1, 24.4 mg kg1, 166 mg kg1, 375 mg kg1, and 17.1 mg kg1 dry weight (d. wt.), respectively. Except Cd, heavy metal concentrations in Australian grown rice were higher than Bangladeshi rice on sale in Australia. However, the concentrations of Cd, Cr, Cu, and Ni in Indian rice on sale in Australia were higher than Australian grown rice. The concentrations of Cu and Ni in Vietnamese rice, and that of Cd, Cr, Cu, Ni, and Pb in Thai rice on sale in Australia were also higher than Australian grown rice. Heavy metal concentrations in Pakistani rice on sale in Australia were substantially lower than that in Australian grown rice. In Australian grown rice varieties, the concentrations of heavy metals were considerably higher in brown rice varieties than white rice varieties, indicating Australian brown rice as a potential source of dietary heavy metals for Australian consumers. The mean concentrations of heavy metals in Australian grown and Bangladeshi vegetables on sale in Australia were also determined. Some of the Australian grown and Bangladeshi vegetables contained heavy metals higher than Australian standard maximum limits indicating them as potential sources of dietary heavy metals for Australian consumers. Further investigation is required to estimate health risks of heavy metals from rice and vegetables consumption for Australian consumers.

Rahman, MM, Alkhouri, H, Tang, F, Che, W, Ge, Q & Ammit, AJ 2014, 'Sphingosine 1-Phosphate Induces Neutrophil Chemoattractant IL-8: Repression by Steroids', PLoS ONE, vol. 9, no. 3, pp. e92466-e92466.
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The bioactive sphingolipid sphingosine 1-phosphate (S1P) is found in increased amounts in the airways of asthmatics. S1P can regulate airway smooth muscle functions associated with asthmatic inflammation and remodeling, including cytokine secretion. To date however, whether S1P induces secretion of an important chemokine responsible for neutrophilia in airway inflammation--IL-8--was unexplored. The aim of this study was to investigate whether S1P induces IL-8 gene expression and secretion to enhance neutrophil chemotaxis in vitro, as well as examine the molecular mechanisms responsible for repression by the corticosteroid dexamethasone. We show that S1P upregulates IL-8 secretion from ASM cells and enhance neutrophil chemotaxis in vitro. The corticosteroid dexamethasone significantly represses IL-8 mRNA expression and protein secretion in a concentration- and time-dependent manner. Additionally, we reveal that S1P-induced IL-8 secretion is p38 MAPK and ERK-dependent and that these key phosphoproteins act on the downstream effector mitogen- and stress-activated kinase 1 (MSK1) to control secretion of the neutrophil chemoattractant cytokine IL-8. The functional relevance of this in vitro data was demonstrated by neutrophil chemotaxis assays where S1P-induced effects can be significantly attenuated by pretreatment with dexamethasone, pharmacological inhibition of p38 MAPK- or ERK-mediated pathways, or by knocking down MSK-1 with siRNA. Taken together, our study reveals the molecular pathways responsible for IL-8 secretion from ASM cells in response to S1P and indicates ways in which the impact on IL-8-driven neutrophilia may be lessened.

Rai, T & Hall, JL 2014, 'Split Leverage: Attacking the Condentiality of Linked Databases by Partitioning', ANZIAM.
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This paper considers the risk of disclosure in linked databases when statistical analysis of micro-data is permitted. The risk of dis- closure needs to be balanced against the utility of the linked data. The current work specifically considers the disclosure risks in permit- ting regression analysis to be performed on linked data. A new attack based on partitioning of the database is presented.

Rajoka, M, Idrees, S, Khalid, S & Ehsan, B 2014, 'Medherb: An Interactive Bioinformatics Database and Analysis Resource for Medicinally Important Herbs', Current Bioinformatics, vol. 9, no. 1, pp. 23-27.
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Ramsay, HA, Richman, MB & Leslie, LM 2014, 'Seasonal Tropical Cyclone Predictions Using Optimized Combinations of ENSO Regions: Application to the Coral Sea Basin', Journal of Climate, vol. 27, no. 22, pp. 8527-8542.
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Abstract This study examines combining ENSO sea surface temperature (SST) regions for seasonal prediction of Coral Sea tropical cyclone (TC) frequency. The Coral Sea averages ~4 TCs per season, but is characterized by strong interannual variability, with 1–9 TCs per season, over the period 1977–2012. A wavelet analysis confirms that ENSO is a key contributor to Coral Sea TC count (TCC) variability. Motivated by the impact of El Niño Modoki on regional climate anomalies, a suite of 38 linear models is constructed and assessed on its ability to predict Coral Sea seasonal TCC. Seasonal predictions of TCC are generated by a leave-one-out cross validation (LOOCV). An important finding is that models made up of multiple tropical Pacific SST regions, such as those that comprise the El Niño Modoki Index (EMI) or the Trans-Niño Index (TNI), perform considerably better than models comprising only single regions, such as Niño-3.4 or Niño-4. Moreover, enhanced (suppressed) TC activity is expected in the Coral Sea when the central Pacific is anomalously cool (warm) and the eastern and western Pacific are anomalously warm (cool) during austral winter. The best cross-validated model has persistent and statistically significantly high correlations with TCC (r &gt; 0.5) at lead times of ~6 months prior to the mean onset of the Coral Sea TC season, whereas correlations based heavily on the widely used Niño-3.4 region are not statistically significant or meaningful (r = 0.09) for the same lead times. Of the 38 models assessed, several optimized forms of the EMI and of the TNI perform best.

Raven, JA & Doblin, MA 2014, 'Active water transport in unicellular algae: where, why, and how', JOURNAL OF EXPERIMENTAL BOTANY, vol. 65, no. 22, pp. 6279-6292.
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Rehaume, LM, Mondot, S, Aguirre de Cárcer, D, Velasco, J, Benham, H, Hasnain, SZ, Bowman, J, Ruutu, M, Hansbro, PM, McGuckin, MA, Morrison, M & Thomas, R 2014, 'ZAP‐70 Genotype Disrupts the Relationship Between Microbiota and Host, Leading to Spondyloarthritis and Ileitis in SKG Mice', Arthritis & Rheumatology, vol. 66, no. 10, pp. 2780-2792.
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ObjectiveThe spondyloarthritides share genetic susceptibility, interleukin‐23 (IL‐23) dependence, and the involvement of microbiota. The aim of the current study was to elucidate how host genetics influence gut microbiota and the relationship between microbiota and organ inflammation in spondyloarthritides.MethodsBALB/c ZAP‐70W163C–mutant (SKG) mice, Toll‐like receptor 4 (TLR‐4)–deficient SKG mice, and wild‐type BALB/c mice were housed under specific pathogen–free conditions. SKG and wild‐type BALB/c mice were maintained under germ‐free conditions, and some of these mice were recolonized with altered Schaedler flora. All of the mice were injected intraperitoneally with microbial β‐1,3‐glucan (curdlan). Arthritis, spondylitis, and ileitis were assessed histologically. Microbiome composition was analyzed in serial fecal samples obtained from mice that were co‐housed beginning at the time of weaning, using 454 pyrosequencing. Infiltrating cells and cytokines in the peritoneal cavity were measured by flow cytometry and enzyme‐linked immunosorbent assay. Cytokine, endoplasmic reticulum (ER) stress marker, and tight junction protein transcription was measured by quantitative real‐time polymerase chain reaction.ResultsMicrobiota content and response to curdlan varied according to whether T cell receptor signal strength was normal or was impaired due to the ZAP‐70W163C mutation. Curdlan triggered acute inflammation regardless of the presence of the SKG allele or microbiota. However, no or limited microbiota content attenuated the severity of arthritis. In contrast, ileal IL‐23 expression, ER stress, lymph node IL‐17A production, goblet cell loss, and ileitis development were microbiota‐dependent. Ileitis but not arthritis was suppressed by microbiota tra...

Reichel, MP, McAllister, MM, Pomroy, WE, Campero, C, Ortega-Mora, LM & Ellis, JT 2014, 'Control options for Neospora caninum - is there anything new or are we going backwards?', PARASITOLOGY, vol. 141, no. 11, pp. 1455-1470.
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Recent work has highlighted and enumerated the economic annual losses due to Neospora caninum abortions worldwide, which should provide strong motivation for the control of bovine neosporosis. However, with the recent withdrawal from sale of the only commercially available vaccine, control options for N. caninum have become more restricted. While researchers continue to work on developing alternative efficacious vaccines, what are the control options presently available for the cattle industries? At the practical level, recommendations for 'Test-and-cull', or 'not breeding from seropositive dams' stand diametrically opposed to alternative options put forward that suggest a primary producer is better advised to keep those cows in the herd that are already seropositive, i.e. assumed to be chronically infected, and indeed those that have already aborted once. Treatment with a coccidiostat has been recommended as the only economically viable option, yet no such treatment has gained official, regulatory approval. Dogs are central to the life cycle of N. caninum and have repeatedly been associated with infection and abortions in cattle by epidemiological studies. Knowledge and understanding of that pivotal role should be able to be put to use in control programmes. The present review canvasses the relevant literature for evidence for control options for N. caninum (some of them proven, many not) and assesses them in the light of the authors' knowledge and experience with control of N. caninum. © Cambridge University Press 2014.

Reichmann, NT, Cassona, CP, Monteiro, JM, Bottomley, AL, Corrigan, RM, Foster, SJ, Pinho, MG & Gruendling, A 2014, 'Differential localization of LTA synthesis proteins and their interaction with the cell division machinery in Staphylococcus aureus', MOLECULAR MICROBIOLOGY, vol. 92, no. 2, pp. 273-286.
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Summary: Lipoteichoic acid (LTA) is an important cell wall component of Gram-positive bacteria. In Staphylococcus aureus it consists of a polyglycerolphosphate-chain that is retained within the membrane via a glycolipid. Using an immunofluorescence approach, we show here that the LTA polymer is not surface exposed in S.aureus, as it can only be detected after digestion of the peptidoglycan layer. S.aureus mutants lacking LTA are enlarged and show aberrant positioning of septa, suggesting a link between LTA synthesis and the cell division process. Using a bacterial two-hybrid approach, we show that the three key LTA synthesis proteins, YpfP and LtaA, involved in glycolipid production, and LtaS, required for LTA backbone synthesis, interact with one another. All three proteins also interacted with numerous cell division and peptidoglycan synthesis proteins, suggesting the formation of a multi-enzyme complex and providing further evidence for the co-ordination of these processes. When assessed by fluorescence microscopy, YpfP and LtaA fluorescent protein fusions localized to the membrane while the LtaS enzyme accumulated at the cell division site. These data support a model whereby LTA backbone synthesis proceeds in S.aureus at the division site in co-ordination with cell division, while glycolipid synthesis takes place throughout the membrane. © 2014 The Authors. Molecular Microbiology published by John Wiley & Sons Ltd.

Reimers, JR & Krausz, E 2014, 'An analytical data inversion method for magnetic circular dichroism spectra dominated by the 'B-term'', PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 16, no. 6, pp. 2315-2322.
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A simple procedure is developed enabling the analytical inversion of an (unpolarized) absorption spectrum combined with a Magnetic Circular Dichroism (MCD) spectrum to resolve two overlapping bands of orthogonal polarization. This method is appropriate when (i) the overlapping transitions are well isolated from other bands, and (ii) when their electronic spacing is large enough so that the 'A-term' and 'C-term' contributions to the MCD spectrum can be ignored and hence only the 'B-term' contribution need be considered. We apply this procedure to assign the Q-band system of chlorophylls, though similar challenges also commonly arise throughout both conventional and X-ray MCD (XMCD) spectroscopy. Analytical data inversion has not previously been possible as the inversion process is two-fold underdetermined. We show that the assumptions of isolated spectra and 'B-term' dominance yields one generally valid constraint, leaving only one quantity unspecified by the experimental data. For some systems, an approximation leading to equal but opposite sign B-term magnitudes of the two components may be reasonable, but for chlorophyllides we find this constraint to be inappropriate. Instead, we constrain a bounded variable controlling the relative absorption strengths. Derived spectral bandshapes of the individual components are shown to be insensitive to its particular value, allowing weak spectral components of one polarization overlapped by intense components of the other to be immediately exposed. This is demonstrated for the chlorophylls, molecules for which the failure to detect such weak features historically led to incorrect proposals for the Q-band assignments. © 2014 the Owner Societies.

Reimers, JR, Cai, Z-L, Kobayashi, R, Raetsep, M, Freiberg, A & Krausz, E 2014, 'Formation of water-chlorophyll clusters in dilute samples of chlorophyll-a in ether at low temperature', PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 16, no. 6, pp. 2323-2330.
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Simultaneously measured absorption (ABS) and magnetic circular dichroism (MCD) spectra of the Q-bands of chlorophyll-a (Chl-a) in ether over 150-186 K reveal that the species that forms at low temperature is a chlorophyll hydrate rather than a diether complex. We have recently proposed a new assignment paradigm for the spectra of chlorophillides which, for the first time, quantitatively accounts for a wide range of observed data. Observations performed at low temperature in ether have historically been very important for the interpretation of the spectra of Chl-a. While our assignment for this system initially anticipated only small spectral changes as the temperature is lowered, significant changes are known to occur. Extensive CAM-B3LYP time-dependent density-functional theory (TD-DFT) calculations verify that the observed spectra of the hydrated species conforms to expectations based on our new assignment, as well as supporting the feasibility of the proposed hydration reactions. © 2014 the Owner Societies.

Rembach, A, Hare, DJ, Doecke, JD, Burnham, SC, Volitakis, I, Fowler, CJ, Cherny, RA, McLean, C, Grimm, R, Martins, R, Ames, D, Masters, CL, Bush, AI & Roberts, BR 2014, 'Decreased serum zinc is an effect of ageing and not Alzheimer's disease', METALLOMICS, vol. 6, no. 7, pp. 1216-1219.
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Ren, D & Leslie, LM 2014, 'Effects of Waves on Tabular Ice-Shelf Calving', Earth Interactions, vol. 18, no. 13, pp. 1-28.
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Abstract As a conveyor belt transferring inland ice to ocean, ice shelves shed mass through large, systematic tabular calving, which also plays a major role in the fluctuation of the buttressing forces. Tabular iceberg calving involves two stages: first is systematic cracking, which develops after the forward-slanting front reaches a limiting extension length determined by gravity–buoyancy imbalance; second is fatigue separation. The latter has greater variability, producing calving irregularity. Whereas ice flow vertical shear determines the timing of the systematic cracking, wave actions are decisive for ensuing viscoplastic fatigue. Because the frontal section has its own resonance frequency, it reverberates only to waves of similar frequency. With a flow-dependent, nonlocal attrition scheme, the present ice model [Scalable Extensible Geoflow Model for Environmental Research-Ice flow submodel (SEGMENT-Ice)] describes an entire ice-shelf life cycle. It is found that most East Antarctic ice shelves have higher resonance frequencies, and the fatigue of viscoplastic ice is significantly enhanced by shoaling waves from both storm surges and infragravity waves (~5 × 10−3 Hz). The two largest embayed ice shelves have resonance frequencies within the range of tsunami waves. When approaching critical extension lengths, perturbations from about four consecutive tsunami events can cause complete separation of tabular icebergs from shelves. For shelves with resonance frequencies matching storm surge waves, future reduction of sea ice may impose much larger deflections from shoaling, storm-generated ocean waves. Although the Ross Ice Shelf (RIS) total mass varies little in the twenty-first century, the mass turnover quickens and the ice conveyor belt is ~40% more efficient by the late twenty-first century, reaching 70 km3 yr−1. The mass distribution shifts oceanward, favoring future tabular calving.

Ren, D, Leslie, LM & Lynch, MJ 2014, 'Trends in Storm-Triggered Landslides over Southern California', Journal of Applied Meteorology and Climatology, vol. 53, no. 2, pp. 217-233.
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AbstractChanges in storm-triggered landslide activity for Southern California in a future warming climate are estimated using an advanced, fully three-dimensional, process-based landslide model, the Scalable and Extensible Geofluid Modeling System for landslides (SEGMENT-Landslide). SEGMENT-Landslide is driven by extreme rainfall projections from the Geophysical Fluid Dynamics Laboratory High Resolution Atmospheric Model (GFDL-HIRAM). Landslide changes are derived from GFDL-HIRAM forcing for two periods: 1) the twentieth century (CNTRL) and 2) the twenty-first century under the moderate Intergovernmental Panel on Climate Change Special Report on Emissions Scenarios A1B enhanced greenhouse gas emissions scenario (EGHG). Here, differences are calculated in landslide frequency and magnitude between the CNTRL and EGHG projections; kernel density estimation (KDE) is used to determine differences in projected landslide locations. This study also reveals that extreme precipitation events in Southern California are strongly correlated with several climate drivers and that GFDL-HIRAM simulates well the southern (relative to Aleutian synoptic systems) storm tracks in El Niño years and the rare (~27-yr recurrence period) hurricane-landfalling events. GFDL-HIRAM therefore can provide satisfactory projections of the geographical distribution, seasonal cycle, and interannual variability of future extreme precipitation events (>50 mm) that have possible landslide consequences for Southern California. Although relatively infrequent, extreme precipitation events contribute most of the annual total precipitation in Southern California. Two findings of this study have major implications for Southern California. First is a possible increase in landslide frequency and areal distribution during the twenty-first century. Second, the KDE reveals three clusters in both the CNTRL and EGHG model mean scarp positions, with a future eastward (inl...

Ren, D, Lynch, M, Leslie, LM & Lemarshall, J 2014, 'Sensitivity of Tropical Cyclone Tracks and Intensity to Ocean Surface Temperature: Four Cases in Four Different Basins', Tellus A: Dynamic Meteorology and Oceanography, vol. 66, no. 1, pp. 24212-24212.
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Ren, J, Ellis, J & Li, J 2014, 'Influenza A HA's conserved epitopes and broadly neutralizing antibodies: A prediction method', JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY, vol. 12, no. 5.
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Ren, J, Liu, Q, Ellis, J & Li, J 2014, 'Tertiary structure-based prediction of conformational B-cell epitopes through B factors', BIOINFORMATICS, vol. 30, no. 12, pp. 264-273.
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Motivation: B-cell epitope is a small area on the surface of an antigen that binds to an antibody. Accurately locating epitopes is of critical importance for vaccine development. Compared with wet-lab methods, computational methods have strong potential for efficient and large-scale epitope prediction for antigen candidates at much lower cost. However, it is still not clear which features are good determinants for accurate epitope prediction, leading to the unsatisfactory performance of existing prediction methods. Method and results: We propose a much more accurate B-cell epitope prediction method. Our method uses a new feature B factor (obtained from X-ray crystallography), combined with other basic physicochemical, statistical, evolutionary and structural features of each residue. These basic features are extended by a sequence window and a structure window. All these features are then learned by a two-stage random forest model to identify clusters of antigenic residues and to remove isolated outliers. Tested on a dataset of 55 epitopes from 45 tertiary structures, we prove that our method significantly outperforms all three existing structure-based epitope predictors. Following comprehensive analysis, it is found that features such as B factor, relative accessible surface area and protrusion index play an important role in characterizing B-cell epitopes. Our detailed case studies on an HIV antigen and an influenza antigen confirm that our second stage learning is effective for clustering true antigenic residues and for eliminating self-made prediction errors introduced by the first-stage learning.

Rice, SA & VerboncoeurIEEE, JP 2014, 'A Comparison of Multipactor Predictions Using Two Popular Secondary Electron Models', IEEE Transactions on Plasma Science, vol. 42, no. 6, pp. 1484-1487.
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Richier, S, Achterberg, EP, Dumousseaud, C, Poulton, AJ, Suggett, DJ, Tyrrell, T, Zubkov, MV & Moore, CM 2014, 'Carbon cycling and phytoplankton responses within highly-replicated shipboard carbonate chemistry manipulation experiments conducted around Northwest European Shelf Seas', Biogeosciences Discussions, vol. 11, no. 3, pp. 3489-3534.
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Abstract. The ongoing oceanic uptake of anthropogenic carbon dioxide (CO2) is significantly altering the carbonate chemistry of seawater, a phenomenon referred to as ocean acidification. Experimental manipulations have been increasingly used to gauge how continued ocean acidification will potentially impact marine ecosystems and their associated biogeochemical cycles in the future; however, results amongst studies, particularly when performed on natural communities, are highly variable, which in part likely reflects inconsistencies in experimental approach. To investigate the potential for identification of more generic responses and greater experimentally reproducibility, we devised and implemented a series of highly replicated (n = 8), short term (2–4 days) multi-level (&amp;geq; 4 conditions) carbonate chemistry/nutrient manipulation experiments on a range of natural microbial communities sampled in Northwest European shelf seas. Carbonate chemistry manipulations and resulting biological responses were found to be highly reproducible within individual experiments and to a lesser extent between geographically different experiments. Statistically robust reproducible physiological responses of phytoplankton to increasing pCO2, characterized by a suppression of net growth for small sized cells (< 10 μm), were observed in the majority of the experiments, irrespective of nutrient status. Remaining between-experiment variability was potentially linked to initial community structure and/or other site-specific environmental factors. Analysis of carbon cycling within the experiments revealed the expected increased sensitivity of carbonate chemistry to biological processes at higher pCO2 and hence lower buffer capacity. The results thus emphasize how biological-chemical feedbacks may be altered in the future ocean.

Richier, S, Achterberg, EP, Dumousseaud, C, Poulton, AJ, Suggett, DJ, Tyrrell, T, Zubkov, MV & Moore, CM 2014, 'Phytoplankton responses and associated carbon cycling during shipboard carbonate chemistry manipulation experiments conducted around Northwest European shelf seas', Biogeosciences, vol. 11, no. 17, pp. 4733-4752.
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Abstract. The ongoing oceanic uptake of anthropogenic carbon dioxide (CO2) is significantly altering the carbonate chemistry of seawater, a phenomenon referred to as ocean acidification. Experimental manipulations have been increasingly used to gauge how continued ocean acidification will potentially impact marine ecosystems and their associated biogeochemical cycles in the future; however, results amongst studies, particularly when performed on natural communities, are highly variable, which may reflect community/environment-specific responses or inconsistencies in experimental approach. To investigate the potential for identification of more generic responses and greater experimentally reproducibility, we devised and implemented a series (n = 8) of short-term (2–4 days) multi-level (≥4 conditions) carbonate chemistry/nutrient manipulation experiments on a range of natural microbial communities sampled in Northwest European shelf seas. Carbonate chemistry manipulations and resulting biological responses were found to be highly reproducible within individual experiments and to a lesser extent between geographically separated experiments. Statistically robust reproducible physiological responses of phytoplankton to increasing pCO2, characterised by a suppression of net growth for small-sized cells (<10 μm), were observed in the majority of the experiments, irrespective of natural or manipulated nutrient status. Remaining between-experiment variability was potentially linked to initial community structure and/or other site-specific environmental factors. Analysis of carbon cycling within the experiments revealed the expected increased sensitivity of carbonate chemistry to biological processes at higher pCO2 and hence lower buffer capacity. The results thus emphasise how biogeochemical feedbacks may be altered in the future ocean.

Richman, MB & Leslie, LM 2014, 'Attribution and Prediction of Maximum Temperature Extremes in SE Australia', Procedia Computer Science, vol. 36, pp. 612-617.
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Roberts, BR, Lim, NKH, McAllum, EJ, Donnelly, PS, Hare, DJ, Doble, PA, Turner, BJ, Price, KA, Lim, SC, Paterson, BM, Hickey, JL, Rhoads, TW, Williams, JR, Kanninen, KM, Hung, LW, Liddell, JR, Grubman, A, Monty, J-F, Llanos, RM, Kramer, DR, Mercer, JFB, Bush, AI, Masters, CL, Duce, JA, Li, Q-X, Beckman, JS, Barnham, KJ, White, AR & Crouch, PJ 2014, 'Oral Treatment with Cu-II(atsm) Increases Mutant SOD1 In Vivo but Protects Motor Neurons and Improves the Phenotype of a Transgenic Mouse Model of Amyotrophic Lateral Sclerosis', JOURNAL OF NEUROSCIENCE, vol. 34, no. 23, pp. 8021-8031.
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Mutations in the metallo-protein Cu/Zn-superoxide dismutase (SOD1) cause amyotrophic lateral sclerosis (ALS) in humans and an expression level-dependent phenotype in transgenic rodents. We show that oral treatment with the therapeutic agent diacetyl-bis(4- methylthiosemicarbazonato)copperII [CuII(atsm)] increased the concentration of mutant SOD1 (SOD1G37R) in ALS model mice, but paradoxically improved locomotor function and survival of the mice. To determine why the mice with increased levels of mutant SOD1 had an improved phenotype, we analyzed tissues by mass spectrometry. These analyses revealed most SOD1 in the spinal cord tissue of the SOD1G37R mice was Cu deficient. Treating with CuII(atsm) decreased the pool of Cu-deficient SOD1 and increased the pool of fully metallated (holo) SOD1. Tracking isotopically enriched 65CuII(atsm) confirmed the increase in holo-SOD1 involved transfer of Cu from CuII(atsm) to SOD1, suggesting the improved locomotor function and survival of the CuII(atsm)-treated SOD1G37R mice involved, at least in part, the ability of the compound to improve the Cu content of the mutant SOD1. This was supported by improved survival of SOD1G37Rmice that expressed thehumangene for theCuuptake protein CTR1. Improving the metal content of mutantSOD1in vivo with CuII(atsm) did not decrease levels of misfolded SOD1. These outcomes indicate the metal content of SOD1 may be a greater determinant of the toxicity of the protein in mutant SOD1-associated forms of ALS than the mutations themselves. Improving the metal content of SOD1 therefore represents a valid therapeutic strategy for treating ALS caused by SOD1.

Roberts, T, Ellis, J, Harkness, J, Marriott, D & Stark, D 2014, 'Treatment failure in patients with chronic Blastocystis infection', JOURNAL OF MEDICAL MICROBIOLOGY, vol. 63, no. 2, pp. 252-257.
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This article reports long-term infection and treatment failure in 18 symptomatic individuals infected with Blastocystis spp. Patients were initially treated with either metronidazole, iodoquinol or triple combination therapy consisting of nitazoxanide, furazolidone and secnidazole. Following treatment, resolution of clinical symptoms did not occur and follow-up testing revealed ongoing infection with the same subtype. Patients then underwent secondary treatment with a variety of antimicrobial agents but remained symptomatic with Blastocystis spp. still present in faeces. Sequencing of the SSU rDNA was completed on all isolates and four subtypes were identified in this group: ST1, ST3, ST4 and ST5. This study highlights the lack of efficacy of several commonly used antimicrobial regimens in the treatment of Blastocystis and the chronic nature of some infections. It also demonstrates the need for further research into treatment options for Blastocystis infection.

Roberts, T, Stark, D, Harkness, J & Ellis, J 2014, 'Update on the pathogenic potential and treatment options for Blastocystis sp', GUT PATHOGENS, vol. 6, pp. 1-9.
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Although Blastocystis is one of the most common enteric parasites, there is still much controversy surrounding the pathogenicity and potential treatment options for this parasite. In this review we look at the evidence supporting Blastocystis as an intestinal pathogen as shown by numerous case studies and several in vivo studies and the evidence against. We describe the chronic nature of some infections and show the role of Blastocystis in immunocompromised patients and the relationship between irritable bowel syndrome and Blastocystis infection. There have been several studies that have suggested that pathogenicity may be subtype related. Metronidazole is the most widely accepted treatment for Blastocystis but several cases of treatment failure and resistance have been described. Other treatment options which have been suggested include paromomycin and trimethroprim- sulfamethoxazole

Robinson, C, Suggett, DJ, Cherukuru, N, Ralph, PJ & Doblin, MA 2014, 'Performance of Fast Repetition Rate fluorometry based estimates of primary productivity in coastal waters', JOURNAL OF MARINE SYSTEMS, vol. 139, pp. 299-310.
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© 2014 Published by Elsevier B.V. Capturing the variability of primary productivity in highly dynamic coastal ecosystems remains a major challenge to marine scientists. To test the suitability of Fast Repetition Rate fluorometry (FRRf) for rapid assessment of primary productivity in estuarine and coastal locations, we conducted a series of paired analyses estimating 14C carbon fixation and primary productivity from electron transport rates with a Fast Repetition Rate fluorometer MkII, from waters on the Australian east coast. Samples were collected from two locations with contrasting optical properties and we compared the relative magnitude of photosynthetic traits, such as the maximum rate of photosynthesis (Pmax), light utilisation efficiency (α) and minimum saturating irradiance (EK) estimated using both methods. In the case of FRRf, we applied recent algorithm developments that enabled electron transport rates to be determined free from the need for assumed constants, as in most previous studies. Differences in the concentration and relative proportion of optically active substances at the two locations were evident in the contrasting attenuation of PAR (400-700nm), blue (431nm), green (531nm) and red (669nm) wavelengths. FRRF-derived estimates of photosynthetic parameters were positively correlated with independent estimates of 14C carbon fixation (Pmax: n=19, R2=0.66; α: n=21, R2=0.77; EK: n=19, R2=0.45; all p<0.05), however primary productivity was frequently underestimated by the FRRf method. Up to 81% of the variation in the relationship between FRRf and 14C estimates was explained by the presence of pico-cyanobacteria and chlorophyll-a biomass, and the proportion of photoprotective pigments, that appeared to be linked to turbidity. We discuss the potential importance of cyanobacteria in influencing the underestimations of FRRf productivity and steps to overcome this potential limitation.

Rodgers, KJ 2014, 'Non-protein amino acids and neurodegeneration: The enemy within', EXPERIMENTAL NEUROLOGY, vol. 253, pp. 192-196.
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Animals, in common with plants and microorganisms, synthesise proteins from a pool of 20 protein amino acids (plus selenocysteine and pyrolysine) (Hendrickson et al., 2004). This represents a small proportion (~2%) of the total number of amino acids known to exist in nature (Bell, 2003). Many 'non-protein' amino acids are synthesised by plants, and in some cases constitute part of their chemical armoury against pathogens, predators or other species competing for the same resources (Fowden et al., 1967). Microorganisms can also use selectively toxic amino acids to gain advantage over competing organisms (Nunn et al., 2010). Since non-protein amino acids (and imino acids) are present in legumes, fruits, seeds and nuts, they are ubiquitous in the diets of human populations around the world. Toxicity to humans is unlikely to have been the selective force for their evolution, but they have the clear potential to adversely affect human health. In this review we explore the links between exposure to non-protein amino acids and neurodegenerative disorders in humans. Environmental factors play a major role in these complex disorders which are predominantly sporadic (Coppede et al., 2006). The discovery of new genes associated with neurodegenerative diseases, many of which code for aggregation-prone proteins, continues at a spectacular pace but little progress is being made in identifying the environmental factors that impact on these disorders. We make the case that insidious entry of non-protein amino acids into the human food chain and their incorporation into protein might be contributing significantly to neurodegenerative damage.

ROSER, DJ, VAN DEN AKKER, B, BOASE, S, HAAS, CN, ASHBOLT, NJ & RICE, SA 2014, 'Pseudomonas aeruginosadose response and bathing water infection', Epidemiology and Infection, vol. 142, no. 3, pp. 449-462.
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SUMMARYPseudomonas aeruginosais the opportunistic pathogen mostly implicated in folliculitis and acute otitis externa in pools and hot tubs. Nevertheless, infection risks remain poorly quantified. This paper reviews disease aetiologies and bacterial skin colonization science to advance dose-response theory development. Three model forms are identified for predicting disease likelihood from pathogen density. Two are based on Furumoto & Mickey's exponential ‘single-hit’ model and predict infection likelihood and severity (lesions/m2), respectively. ‘Third-generation’, mechanistic, dose-response algorithm development is additionally scoped. The proposed formulation integrates dispersion, epidermal interaction, and follicle invasion. The review also details uncertainties needing consideration which pertain to water quality, outbreaks, exposure time, infection sites, biofilms, cerumen, environmental factors (e.g. skin saturation, hydrodynamics), and whetherP. aeruginosais endogenous or exogenous. The review's findings are used to propose a conceptual infection model and identify research priorities including pool dose-response modelling, epidermis ecology and infection likelihood-based hygiene management.

Roudnew, B, Lavery, TJ, Seymour, JR, Jeffries, TC & Mitchell, JG 2014, 'Variability in Bacteria and Virus-Like Particle Abundances During Purging of Unconfined Aquifers', GROUND WATER, vol. 52, no. 1, pp. 118-124.
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Standard methodologies for sampling the physicochemical conditions of groundwater recommend purging a bore for three bore volumes to avoid sampling the stagnant water within a bore and instead gain samples representative of the aquifer. However, there are currently no methodological standards addressing the amount of purging required to gain representative biological samples to assess groundwater bacterial and viral abundances. The objective of this study was to examine how bacterial and viral abundances change during the purging of bore volumes. Six bores infiltrating into unconfined aquifers were pumped for five or six bore volumes each and bacteria and virus-like particles (VLPs) were enumerated from each bore volume using flow cytometry. In examination of the individual bores trends in bacterial abundances were observed to increase, decrease, or remain constant with each purged bore volume. Furthermore, triplicates taken at each bore volume indicated substantial variations in VLP and bacterial abundances that are often larger than the differences between bore volumes. This indicates a high level of small scale heterogeneity in microbial community abundance in groundwater samples, and we suggest that this may be an intrinsic feature of bore biology. The heterogeneity observed may be driven by bottom up processes (variability in the distribution of organic and inorganic nutrients), top-down processes (grazing and viral lysis), physical heterogeneities in the bore, or technical artifacts associated with the purging process. We suggest that a more detailed understanding of the ecology underpinning this variability is required to adequately describe the microbiological characteristics of groundwater ecosystems.

Sachse, K, Laroucau, K, Riege, K, Wehner, S, Dilcher, M, Creasy, HH, Weidmann, M, Myers, G, Vorimore, F, Vicari, N, Magnino, S, Liebler-Tenorio, E, Ruettger, A, Bavoil, PM, Hufert, FT, Rosselló-Móra, R & Marz, M 2014, 'Evidence for the existence of two new members of the family Chlamydiaceae and proposal of Chlamydia avium sp. nov. and Chlamydia gallinacea sp. nov.', Systematic and Applied Microbiology, vol. 37, no. 2, pp. 79-88.
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Sackett, O, Armand, L, Beardall, J, Hill, R, Doblin, M, Connelly, C, Howes, J, Stuart, B, Ralph, P & Heraud, P 2014, 'Taxon-specific responses of Southern Ocean diatoms to Fe enrichment revealed by synchrotron radiation FTIR microspectroscopy', BIOGEOSCIENCES, vol. 11, no. 20, pp. 5795-5808.
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© 2014 Author(s). Photosynthesis by marine diatoms contributes substantially to global biogeochemical cycling and ecosystem productivity. It is widely accepted that diatoms are extremely sensitive to changes in Fe availability, with numerous in situ experiments demonstrating rapid growth and increased export of elements (e.g. C, Si and Fe) from surface waters as a result of Fe addition. Less is known about the effects of Fe enrichment on the phenotypes of diatoms, such as associated changes in nutritional value-furthermore, data on taxon-specific responses are almost non-existent. Enhanced supply of nutrient-rich waters along the coast of the subantarctic Kerguelen Island provide a valuable opportunity to examine the responses of phytoplankton to natural Fe enrichment. Here we demonstrate the use of synchrotron radiation Fourier Transform Infrared (SR-FTIR) microspectroscopy to analyse changes in the macromolecular composition of diatoms collected along the coast and plateau of Kerguelen Island, Southern Ocean. SR-FTIR microspectroscopy enabled the analysis of individual diatom cells from mixed communities of field-collected samples, thereby providing insight into in situ taxon-specific responses in relation to changes in Fe availability. Phenotypic responses were taxon-specific in terms of intraspecific variability and changes in proteins, amino acids, phosphorylated molecules, silicate/silicic acid and carbohydrates. In contrast to some previous studies, silicate/silicic acid levels increased under Fe enrichment, in conjunction with increases in carbohydrate stores. The highly abundant taxon Fragilariopsis kerguelensis displayed a higher level of phenotypic plasticity than Pseudo-nitzschia spp., while analysis of the data pooled across all measured taxa showed different patterns in macromolecular composition compared to those for individual taxon. This study demonstrates that taxon-specific responses to Fe enrichment may not always be accurately refle...

Sackett, O, Armand, L, Beardall, J, Hill, R, Doblin, M, Connelly, C, Howes, J, Stuart, B, Ralph, P & Heraud, P 2014, 'Taxon-specific responses of Southern Ocean diatoms to Fe enrichment revealed by synchrotron radiation FTIR microspectroscopy', Biogeosciences Discussions, vol. 11, no. 5, pp. 7327-7357.
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Abstract. Photosynthesis by marine diatoms contributes substantially to global biogeochemical cycling and ecosystem productivity. It is widely accepted that diatoms are extremely sensitive to changes in Fe availability, with numerous in situ experiments demonstrating rapid growth and increased export of elements (e.g. C, Si and Fe) from surface waters as a result of Fe addition. Less is known about the effects of Fe enrichment on the phenotypes of diatoms, such as associated changes in nutritional value, furthermore data on taxon-specific responses is almost non-existent. Enhanced supply of nutrient-rich waters along the coast of the subantarctic Kerguelen Island provide a valuable opportunity to examine the responses of phytoplankton to natural Fe enrichment. Here we demonstrate the use of synchrotron radiation Fourier Transform Infrared (SR-FTIR) microspectroscopy to analyse changes in the macromolecular composition of diatoms collected along the coast and plateau of Kerguelen Island, Southern Ocean. SR-FTIR microspectroscopy enabled the analysis of individual diatom cells from mixed communities of field-collected samples, thereby providing insight into in situ taxon-specific responses in relation to changes in Fe availability. Phenotypic responses were taxon-specific in terms of intraspecific variability and changes in proteins, amino acids, phosphorylated molecules, silicate and carbohydrates. In contrast to some previous studies, silicate levels increased under Fe enrichment, in conjunction with increases in carbohydrate stores. The highly abundant taxon Fragilariopsis kerguelensis displayed a higher level of phenotypic plasticity than Pseudo-nitzschia spp., while analysis of the data pooled across all measured taxa showed different patterns in macromolecular composition compared to those for individual taxon. This study demonstrates that taxon-specific responses to Fe enrichment may not always be accurately reflected by bulk community meas...

Saffari, M, Pakpour, AH, Mohammadi-Zeidi, I, Samadi, M & Chen, H 2014, 'Long-term effect of motivational interviewing on dietary intake and weight loss in Iranian obese/overweight women.', Health Promot Perspect, vol. 4, no. 2, pp. 206-213.
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BACKGROUND: This study aimed to determine whether motivational interviewing (MI) could change dietary habit and body mass index (BMI) in obese/overweight women. METHODS: A cluster-randomized controlled study was performed in four health centers in Qazvin, central Iran. In total, 327 obese/overweight women were selected by a multi-stage sampling method and randomly assigned into control and experimental groups. Food frequency (using questionnaire; FFQ), BMI, and metabolic markers including blood pressure, total serum cholesterol and fasting blood glucose levels were measured in all participants. Data were collected twice (before and one year after the MI interventions). Data were analyzed using student t-test, and Stepwise Linear Regression. RESULTS: There was a significant increase in daily consumption of dietary fiber, whole grain products, fruits and vegetables in the MI group (P<0.05). The consumption of meat product, total fat, saturated fat, carbohydrate and total energy intake were also significantly reduced after MI intervention (P<0.05). As a result, body weight and BMI were significantly reduced in the intervention group compared to the control group (P<0.05). CONCLUSION: MI is suggested to be an effective strategy to change life style and reduce BMI in overweight/obese women in the long term. This effect needs to be further investigated in different gender and age populations.

Saffari, M, Pakpour, AH, Mohammadi-Zeidi, S, Samadi, M & Chen, H 2014, 'Long-Term Effect of Motivational Interviewing on Dietary Intake and Weight Loss in Iranian Obese/Overweight Women', Health Promot Perspect, vol. 2014, no. 2, pp. 206-213.

Sait, M, Livingstone, M, Clark, EM, Wheelhouse, N, Spalding, L, Markey, B, Magnino, S, Lainson, FA, Myers, GSA & Longbottom, D 2014, 'Genome sequencing and comparative analysis of three Chlamydia pecorum strains associated with different pathogenic outcomes', BMC Genomics, vol. 15, no. 1, pp. 1-15.
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BACKGROUND: Chlamydia pecorum is the causative agent of a number of acute diseases, but most often causes persistent, subclinical infection in ruminants, swine and birds. In this study, the genome sequences of three C. pecorum strains isolated from the faeces of a sheep with inapparent enteric infection (strain W73), from the synovial fluid of a sheep with polyarthritis (strain P787) and from a cervical swab taken from a cow with metritis (strain PV3056/3) were determined using Illumina/Solexa and Roche 454 genome sequencing. RESULTS: Gene order and synteny was almost identical between C. pecorum strains and C. psittaci. Differences between C. pecorum and other chlamydiae occurred at a number of loci, including the plasticity zone, which contained a MAC/perforin domain protein, two copies of a >3400 amino acid putative cytotoxin gene and four (PV3056/3) or five (P787 and W73) genes encoding phospholipase D. Chlamydia pecorum contains an almost intact tryptophan biosynthesis operon encoding trpABCDFR and has the ability to sequester kynurenine from its host, however it lacks the genes folA, folKP and folB required for folate metabolism found in other chlamydiae. A total of 15 polymorphic membrane proteins were identified, belonging to six pmp families. Strains possess an intact type III secretion system composed of 18 structural genes and accessory proteins, however a number of putative inc effector proteins widely distributed in chlamydiae are absent from C. pecorum. Two genes encoding the hypothetical protein ORF663 and IncA contain variable numbers of repeat sequences that could be associated with persistence of infection. CONCLUSIONS: Genome sequencing of three C. pecorum strains, originating from animals with different disease manifestations, has identified differences in ORF663 and pseudogene content between strains and has identified genes and metabolic traits that may influence intracellular survival, pathogenicity and evasion of the host immune system.

Salavati-Niasari, M, Behfard, Z & Maddahfar, M 2014, 'Controllable synthesis of Bi2S3 via a simple hydrothermal approach starting from an inorganic precursor', Journal of Industrial and Engineering Chemistry, vol. 20, no. 6, pp. 4066-4075.
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Sandanayake, S & Langford, SJ 2014, 'Crown Ether Derivatised Pyromellitic Diimides', Australian Journal of Chemistry, vol. 67, no. 9, pp. 1264-1264.
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Pyromellitic diimide functionalised on the aromatic core with azacrown ethers have been synthesised and characterised by analytical methods including X-ray crystallography. Changes in their UV-vis spectra by the addition of metal salts have been investigated.

Sandstrom, RG, Shimoni, O, Martin, AA & Aharonovich, I 2014, 'Study of narrowband single photon emitters in polycrystalline diamond films', APPLIED PHYSICS LETTERS, vol. 105, no. 18.
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© 2014 AIP Publishing LLC. Quantum information processing and integrated nanophotonics require robust generation of single photon emitters on demand. In this work, we demonstrate that diamond films grown on a silicon substrate by microwave plasma chemical vapor deposition can host bright, narrowband single photon emitters in the visible - near infra-red spectral range. The emitters possess fast lifetime (∼ several ns), absolute photostability, and exhibit full polarization at excitation and emission. Pulsed and continuous laser excitations confirm their quantum behaviour at room temperature, while low temperature spectroscopy is performed to investigate inhomogeneous broadening. Our results advance the knowledge of solid state single photon sources and open pathways for their practical implementation in quantum communication and quantum information processing.

Sargent-Cox, KA, Anstey, KJ & Luszcz, MA 2014, 'Longitudinal Change of Self-Perceptions of Aging and Mortality', The Journals of Gerontology Series B: Psychological Sciences and Social Sciences, vol. 69, no. 2, pp. 168-173.
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Sarkar, A, Mallick, BK, Staudenmayer, J, Pati, D & Carroll, RJ 2014, 'Bayesian Semiparametric Density Deconvolution in the Presence of Conditionally Heteroscedastic Measurement Errors', Journal of Computational and Graphical Statistics, vol. 23, no. 4, pp. 1101-1125.
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© 2014, © 2014 American Statistical Association, Institute of Mathematical Statistics, and Interface Foundation of North America. We consider the problem of estimating the density of a random variable when precise measurements on the variable are not available, but replicated proxies contaminated with measurement error are available for sufficiently many subjects. Under the assumption of additive measurement errors this reduces to a problem of deconvolution of densities. Deconvolution methods often make restrictive and unrealistic assumptions about the density of interest and the distribution of measurement errors, for example, normality and homoscedasticity and thus independence from the variable of interest. This article relaxes these assumptions and introduces novel Bayesian semiparametric methodology based on Dirichlet process mixture models for robust deconvolution of densities in the presence of conditionally heteroscedastic measurement errors. In particular, the models can adapt to asymmetry, heavy tails, and multimodality. In simulation experiments, we show that our methods vastly outperform a recent Bayesian approach based on estimating the densities via mixtures of splines. We apply our methods to data from nutritional epidemiology. Even in the special case when the measurement errors are homoscedastic, our methodology is novel and dominates other methods that have been proposed previously. Additional simulation results, instructions on getting access to the dataset and R programs implementing our methods are included as part of online supplementary materials.

Sarkar, A, Pati, D, Mallick, BK & Carroll, RJ 2014, 'Bayesian Semiparametric Multivariate Density Deconvolution', Journal of the American Statistical Association, vol. 113, no. 521, pp. 401-416.
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We consider the problem of multivariate density deconvolution when theinterest lies in estimating the distribution of a vector-valued random variablebut precise measurements of the variable of interest are not available,observations being contaminated with additive measurement errors. The existingsparse literature on the problem assumes the density of the measurement errorsto be completely known. We propose robust Bayesian semiparametric multivariatedeconvolution approaches when the measurement error density is not known butreplicated proxies are available for each unobserved value of the randomvector. Additionally, we allow the variability of the measurement errors todepend on the associated unobserved value of the vector of interest throughunknown relationships which also automatically includes the case ofmultivariate multiplicative measurement errors. Basic properties of finitemixture models, multivariate normal kernels and exchangeable priors areexploited in many novel ways to meet the modeling and computational challenges.Theoretical results that show the flexibility of the proposed methods areprovided. We illustrate the efficiency of the proposed methods in recoveringthe true density of interest through simulation experiments. The methodology isapplied to estimate the joint consumption pattern of different dietarycomponents from contaminated 24 hour recalls.

Scanes, E, Parker, LM, O’Connor, WA & Ross, PM 2014, 'Mixed Effects of Elevated pCO2 on Fertilisation, Larval and Juvenile Development and Adult Responses in the Mobile Subtidal Scallop Mimachlamys asperrima (Lamarck, 1819)', PLoS ONE, vol. 9, no. 4, pp. e93649-e93649.
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Ocean acidification is predicted to have severe consequences for calcifying marine organisms especially molluscs. Recent studies, however, have found that molluscs in marine environments with naturally elevated or fluctuating CO2 or with an active, high metabolic rate lifestyle may have a capacity to acclimate and be resilient to exposures of elevated environmental pCO2. The aim of this study was to determine the effects of near future concentrations of elevated pCO2 on the larval and adult stages of the mobile doughboy scallop, Mimachlamys asperrima from a subtidal and stable physio-chemical environment. It was found that fertilisation and the shell length of early larval stages of M. asperrima decreased as pCO2 increased, however, there were less pronounced effects of elevated pCO2 on the shell length of later larval stages, with high pCO2 enhancing growth in some instances. Byssal attachment and condition index of adult M. asperrima decreased with elevated pCO2, while in contrast there was no effect on standard metabolic rate or pHe. The responses of larval and adult M. asperrima to elevated pCO2 measured in this study were more moderate than responses previously reported for intertidal oysters and mussels. Even this more moderate set of responses are still likely to reduce the abundance of M. asperrima and potentially other scallop species in the world's oceans at predicted future pCO2 levels.

Schrameyer, V, Wangpraseurt, D, Hill, R, Kuehl, M, Larkum, AWD & Ralph, PJ 2014, 'Light Respiratory Processes and Gross Photosynthesis in Two Scleractinian Corals', PLOS ONE, vol. 9, no. 10.
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© 2014 Schrameyer et al. The light dependency of respiratory activity of two scleractinian corals was examined using O2 microsensors and CO2 exchange measurements. Light respiration increased strongly but asymptotically with elevated irradiance in both species. Light respiration in Pocillopora damicornis was higher than in Pavona decussata under low irradiance, indicating species-specific differences in light-dependent metabolic processes. Overall, the coral P. decussata exhibited higher CO2 uptake rates than P. damicornis over the experimental irradiance range. P. decussata also harboured twice as many algal symbionts and higher total protein biomass compared to P. damicornis, possibly resulting in self-shading of the symbionts and/or changes in host tissue specific light distribution. Differences in light respiration and CO2 availability could be due to host-specific characteristics that modulate the symbiont microenvironment, its photosynthesis, and hence the overall performance of the coral holobiont.

Scott, NE, Marzook, NB, Cain, JA, Solis, N, Thaysen-Andersen, M, Djordjevic, SP, Packer, NH, Larsen, MR & Cordwell, SJ 2014, 'Comparative Proteomics and Glycoproteomics Reveal Increased N-Linked Glycosylation and Relaxed Sequon Specificity in Campylobacter jejuni NCTC11168 O', Journal of Proteome Research, vol. 13, no. 11, pp. 5136-5150.
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Campylobacter jejuni is a major cause of bacterial gastroenteritis. C. jejuni encodes a protein glycosylation (Pgl) locus responsible for the N-glycosylation of membrane-associated proteins. We examined two variants of the genome sequenced strain NCTC11168: O, a representative of the original clinical isolate, and GS, a laboratory-adapted relative of O. Comparative proteomics by iTRAQ and two-dimensional liquid chromatography coupled to tandem mass spectrometry (2D-LC-MS/MS) allowed the confident identification of 1214 proteins (73.9% of the predicted C. jejuni proteome), of which 187 were present at statistically significant altered levels of abundance between variants. Proteins associated with the O variant included adhesins (CadF and FlpA), proteases, capsule biosynthesis, and cell shape determinants as well as six proteins encoded by the Pgl system, including the PglK flippase and PglB oligosaccharyltransferase. Lectin blotting highlighted specific glycoproteins more abundant in NCTC11168 O, whereas others remained unaltered. Hydrophilic interaction liquid chromatography (HILIC) and LC-MS/MS identified 30 completely novel glycosites from 15 proteins. A novel glycopeptide from a 14 kDa membrane protein (Cj0455c) was identified that did not contain the C. jejuni N-linked sequon D/E-X-N-X-S/T (X ≠ Pro) but that instead contained a sequon with leucine at the -2 position. Occupied atypical sequons were also observed in Cj0958c (OxaA; Gln at the -2 position) and Cj0152c (Ala at the +2 position). The relative O and GS abundances of 30 glycopeptides were determined by label-free quantitation, which revealed a >100-fold increase in the atypical glycopeptide from Cj0455c in isolate O. Our data provide further evidence for the importance of the Pgl system in C. jejuni.

Scott, PD, Bartkow, M, Blockwell, SJ, Coleman, HM, Khan, SJ, Lim, R, McDonald, JA, Nice, H, Nugegoda, D, Pettigrove, V, Tremblay, LA, Warne, MSJ & Leusch, FDL 2014, 'A National Survey of Trace Organic Contaminants in Australian Rivers', Journal of Environmental Quality, vol. 43, no. 5, pp. 1702-1712.
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© American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America. Trace organic contaminant (TrOC) studies in Australia have, to date, focused on wastewater effluents, leaving a knowledge gap of their occurrence and risk in freshwater environments. This study measured 42 TrOCs including industrial compounds, pesticides, and pharmaceuticals and personal care products by liquid chromatography tandem mass spectrometry at 73 river sites across Australia quarterly for 1 yr. Trace organic contaminants were found in 92% of samples, with a median of three compounds detected per sample (maximum 18). The five most commonly detected TrOCs were the pharmaceuticals salicylic acid (82%, maximum = 1530 ng/L), paracetamol (also known as acetaminophen; 45%, maximum = 7150 ng/L), and carbamazepine (27%, maximum = 682 ng/L), caffeine (65%, maximum = 3770 ng/L), and the flame retardant tris(2- chloroethyl) phosphate (44%, maximum = 184 ng/L). Pesticides were detected in 28% of the samples. To determine the risk posed by the detected TrOCs to the aquatic environment, hazard quotients were calculated by dividing the maximum concentration detected for each compound by the predicted noeffect concentrations. Three of the 42 compounds monitored (the pharmaceuticals carbamazepine and sulfamethoxazole and the herbicide simazine) had a hazard quotient >1, suggesting that they may be causing adverse effects at the most polluted sites. A further 10 compounds had hazard quotients >0.1, indicating a potential risk; these included four pharmaceuticals, three personal care products, and three pesticides. Most compounds had hazard quotients significantly <0.1. The number of TrOCs measured in this study was limited and further investigations are required to fully assess the risk posed by complex mixtures of TrOCs on exposed biota.

Scott, PD, Bartkow, M, Blockwell, SJ, Coleman, HM, Khan, SJ, Lim, R, McDonald, JA, Nice, H, Nugegoda, D, Pettigrove, V, Tremblay, LA, Warne, MSJ & Leusch, FDL 2014, 'An assessment of endocrine activity in Australian rivers using chemical and in vitro analyses', Environmental Science and Pollution Research, vol. 21, no. 22, pp. 12951-12967.
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Scuderi, S, D’Amico, AG, Castorina, A, Federico, C, Marrazzo, G, Drago, F, Bucolo, C & D’Agata, V 2014, 'Davunetide (NAP) Protects the Retina Against Early Diabetic Injury by Reducing Apoptotic Death', Journal of Molecular Neuroscience, vol. 54, no. 3, pp. 395-404.
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Seidel, D, Martínez, I, Taddeo, S, Joseph, M, Carroll, R, Haub, M, Walter, J & Turner, N 2014, 'A polyphenol‐rich sorghum cereal alters colon microbiota and plasma metabolites in overweight subjects (270.7)', The FASEB Journal, vol. 28, no. S1.
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Diet has the potential to impact gut microbiota and metabolism, with implications for obesity and inflammation. We have shown that polyphenol‐rich sumac sorghum (contains condensed tannins) alters microbial populations and metabolites in rats. The goal of this study was to determine if similar effects occur in overweight subjects predisposed to metabolic syndrome (MS). Subjects (n=24) were randomized in a crossover design with high (100 g/d) and low (50 g/d) intakes (4 wk) of sumac sorghum cereal incorporated in their normal diets. Sumac sorghum induced compositional changes in the fecal microbiota, such as an increase (q=0.076) in anti‐inflammatory Faecalibacterium prausnitzii species. Untargeted metabolomic analysis of plasma revealed reductions in amino acid (AA) metabolites as well as increases in microbially‐derived aromatic AA and polyphenol metabolites. 3‐hydroxyhippurate, a product of chlorogenic acid metabolism shown to be reduced in individuals with impaired glucose tolerance, was increased (q=0.0145) following sumac sorghum consumption. Three gamma‐glutamyl AAs produced by gamma‐glutamyl transferase, a biomarker for MS and cardiovascular risk, were decreased (q<0.05) with the 100 g intake. These data suggest sumac sorghum beneficially modulates gut bacteria and their metabolites, which may contribute to reduced inflammation and improved glucose sensitivity.Grant Funding Source: Supported by United Sorghum Checkoff Program R0002‐11.

Setzpfandt, F, Solntsev, AS, Neshev, DN, Pertsch, T, Sohler, W & Schiek, R 2014, 'Temporal dynamics of spatially localized waves in quadratic nonlinear waveguide arrays', Physical Review A, vol. 89, no. 3.
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Seymour, JR 2014, 'A sea of microbes: the diversity and activity of marine microorganisms', Microbiology Australia, vol. 35, no. 4, pp. 183-183.
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Covering 70% of the earth’s surface, with an average depth of 3.6 km, the ocean’s total volume of 1.3 billion cubic kilometres represents perhaps the largest inhabitable space in the biosphere. Within this vast ecosystem, 90% of all living biomass is microbial. Indeed, seawater from all marine environments, ranging from the warm and sunlit upper ocean to the cold, dark and anoxic deep sea floor, and from the tropics to the arctic, is teeming with microbial life. A single teaspoon of seawater typically contains over 50 million viruses, 5 million Bacteria, 100,000 Archaea and 50,000 eukaryotic microbes. The numerical importance of these microbes is matched only by their ecological and biogeochemical significance. By performing the bulk of oceanic primary production and mediating key chemical transformation processes, planktonic microbes form the base of the marine food-web and are the engines that drive the ocean’s major biogeochemical cycles (Figure 1). While marine microbes are the dominant biological feature throughout the entire water column and within ocean sediments, as well as being important symbionts and pathogens of marine animals and plants, this review will focus on the activity and diversity of microbes inhabiting seawater in the upper sun-lit depths of the global ocean.

Shahid, M, El Saliby, I, McDonagh, A, Tijing, LD, Kim, J-H & Shon, HK 2014, 'Synthesis and characterisation of potassium polytitanate for photocatalytic degradation of crystal violet', Journal of Environmental Sciences, vol. 26, no. 11, pp. 2348-2354.
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Potassium titanate nanostructures were synthesised by hydrothermal treatment of TiO2 (P25) in KOH and H2O2. As-produced powders were characterised by scanning electron microscopy, energy-dispersive X-ray spectroscopy, transmission electron microscopy, X-ray diffraction, and nitrogen adsorption-desorption methods. Longitudinally-oriented-wire-like structures with a length up to several micrometres and diameters ranging from 10 to 30 nm were obtained. Larger size fibrous nanowires resulting from the hydrothermal treatment showed high affinity in adsorbing crystal violet (CV), which was mainly due to their high surface area. The photocatalytic bleaching of CV solution revealed that the wires are photoactive under ultraviolet light irradiation. Macroporous nanowires are considered as effective adsorbents of CV, capable of photocatalytic degradation, and they can be easily separated from the solution by settling.

Shahid, M, Saliby, IE, McDonagh, A, Kim, J-H & Shon, HK 2014, 'Photodesorption of specific organic compounds from titanium dioxide particles in aqueous media', Desalination and Water Treatment, vol. 52, no. 4-6, pp. 867-872.
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This study investigates the photodesorption of organic compounds (beef extract, peptone, humic acid, tannic acid, sodium lignin sulphonate, sodium lauryl sulphate, arabic gum powder and arabic acid) from TiO2 (1 g/L in water, pH 7). After a period to reach adsorption equilibrium, photodesorption experiments were conducted in a recirculated reactor at a constant flow rate of 150 mL/min with a UV light intensity of 24 W. Photodesorption was observed only for sodium lauryl sulphate (50%), sodium lignin sulphonate (43.47%), beef extract (20.35%) and tannic acid (10.5%) indicating that photodesorption is specific to some organic compounds but not to all. Using liquid chromatography-organic carbon detection, untreated beef extract and sodium lignin sulphonate were found to contain significant amounts of humic substances (∼1,000 g/mol), which decreased in concentration after dark phase adsorption, while a significant increase in low molecular weight (<350 g/mol) concentrations was observed after photodesorption. UV-treated sodium lauryl sulphate photodesorbed to give both higher molecular weight (HMW) and lower molecular weight (LMW) organics. Thus, the HMW fractions of organic compounds decomposed into smaller compounds after UV irradiation, which subsequently desorbed from TiO2 surface. However, untreated tannic acid contained a larger proportion of LMW acids, which shows a high adsorption affinity to TiO2 during adsorption and poorly desorbs upon irradiation.

Shanley, TW, Martin, AA, Aharonovich, I & Toth, M 2014, 'Localized chemical switching of the charge state of nitrogen-vacancy luminescence centers in diamond', APPLIED PHYSICS LETTERS, vol. 105, no. 6.
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We present a direct-write chemical technique for controlling the charge state of near-surface nitrogen vacancy centers (NVs) in diamond by surface fluorination. Fluorination of H-terminated diamond is realized by electron beam stimulated desorption of H2O in the presence of NF3 and verified with environmental photoyield spectroscopy (EPYS) and photoluminescence (PL) spectroscopy. PL spectra of shallow NVs in H- and F-terminated nanodiamonds show the expected dependence of the NV charge state on their energetic position with respect to the Fermi-level. EPYS reveals a corresponding difference between the ionization potential of H- and F-terminated diamond. The electron beam fluorination process is highly localized and can be used to fluorinate H-terminated diamond, and to increase the population of negatively charged NV centers. © 2014 AIP Publishing LLC.

Shen, H-H, Leyton, DL, Shiota, T, Belousoff, MJ, Noinaj, N, Lu, J, Holt, SA, Tan, K, Selkrig, J, Webb, CT, Buchanan, SK, Martin, LL & Lithgow, T 2014, 'Reconstitution of a nanomachine driving the assembly of proteins into bacterial outer membranes', Nature Communications, vol. 5, no. 1.
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Shi, H, Li, L, Eamus, D, Cleverly, J, Huete, A, Beringer, J, Yu, Q, Van Gorsel, E & Hutley, L 2014, 'Intrinsic climate dependency of ecosystem light and water-use-efficiencies across Australian biomes', ENVIRONMENTAL RESEARCH LETTERS, vol. 9, no. 10, pp. 104002-104002.
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© 2014 IOP Publishing Ltd. The sensitivity of ecosystem gross primary production (GPP) to availability of water and photosynthetically active radiation (PAR) differs among biomes. Here we investigated variations of ecosystem light-use-efficiency (eLUE: GPP/PAR) and water-use-efficiency (eWUE: GPP/evapotranspiration) among seven Australian eddy covariance sites with differing annual precipitation, species composition and temperature. Changes to both eLUE and eWUE were primarily correlated with atmospheric vapor pressure deficit (VPD) at multiple temporal scales across biomes, with minor additional correlations observed with soil moisture and temperature. The effects of leaf area index on eLUE and eWUE were also relatively weak compared to VPD, indicating an intrinsic dependency of eLUE and eWUE on climate. Additionally, eLUE and eWUE were statistically different for biomes between summer and winter, except eWUE for savannas and the grassland. These findings will improve our understanding of how light- and water-use traits in Australian ecosystems may respond to climate change.

Shimizu, M, Fujimoto, R, Ying, H, Pu, Z-J, Ebe, Y, Kawanabe, T, Saeki, N, Taylor, JM, Kaji, M, Dennis, ES & Okazaki, K 2014, 'Identification of candidate genes for fusarium yellows resistance in Chinese cabbage by differential expression analysis', PLANT MOLECULAR BIOLOGY, vol. 85, no. 3, pp. 247-257.
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Shimoni, O, Cervenka, J, Karle, TJ, Fox, K, Gibson, BC, Tomljenovic-Hanic, S, Greentree, AD & Prawer, S 2014, 'Development of a Templated Approach to Fabricate Diamond Patterns on Various Substrates', ACS Applied Materials & Interfaces, vol. 6, no. 11, pp. 8894-8902.
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We demonstrate a robust templated approach to pattern thin films of chemical vapor deposited nanocrystalline diamond grown from monodispersed nanodiamond (mdND) seeds. The method works on a range of substrates, and we herein demonstrate the method using silicon, aluminum nitride (AlN), and sapphire substrates. Patterns are defined using photo- and e-beam lithography, which are seeded with mdND colloids and subsequently introduced into microwave assisted chemical vapor deposition reactor to grow patterned nanocrystalline diamond films. In this study, we investigate various factors that affect the selective seeding of different substrates to create high quality diamond thin films, including mdND surface termination, zeta potential, surface treatment, and plasma cleaning. Although the electrostatic interaction between mdND colloids and substrates is the main process driving adherence, we found that chemical reaction (esterification) or hydrogen bonding can potentially dominate the seeding process. Leveraging the knowledge on these different interactions, we optimize fabrication protocols to eliminate unwanted diamond nucleation outside the patterned areas. Furthermore, we have achieved the deposition of patterned diamond films and arrays over a range of feature sizes. This study contributes to a comprehensive understanding of the mdND-substrate interaction that will enable the fabrication of integrated nanocrystalline diamond thin films for microelectronics, sensors, and tissue culturing applications. © 2014 American Chemical Society.

Si, W, Mönch, I, Yan, C, Deng, J, Li, S, Lin, G, Han, L, Mei, Y & Schmidt, OG 2014, 'A Single Rolled‐Up Si Tube Battery for the Study of Electrochemical Kinetics, Electrical Conductivity, and Structural Integrity', Advanced Materials, vol. 26, no. 47, pp. 7973-7978.
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Siboni, N, Abrego, D, Motti, CA, Tebben, J & Harder, T 2014, 'Gene Expression Patterns during the Early Stages of Chemically Induced Larval Metamorphosis and Settlement of the Coral Acropora millepora', PLOS ONE, vol. 9, no. 3, pp. 1-9.
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The morphogenetic transition of motile coral larvae into sessile primary polyps is triggered and genetically programmed upon exposure to environmental biomaterials, such as crustose coralline algae (CCA) and bacterial biofilms. Although the specific chemical cues that trigger coral larval morphogenesis are poorly understood there is much more information available on the genes that play a role in this early life phase. Putative chemical cues from natural biomaterials yielded defined chemical samples that triggered different morphogenetic outcomes: an extract derived from a CCA-associated Pseudoalteromonas bacterium that induced metamorphosis, characterized by non-attached metamorphosed juveniles; and two fractions of the CCA Hydrolithon onkodes (Heydrich) that induced settlement, characterized by attached metamorphosed juveniles. In an effort to distinguish the genes involved in these two morphogenetic transitions, competent larvae of the coral Acropora millepora were exposed to these predictable cues and the expression profiles of 47 coral genes of interest (GOI) were investigated after only 1 hour of exposure using multiplex RT-qPCR. Thirty-two GOI were differentially expressed, indicating a putative role during the early regulation of morphogenesis. The most striking differences were observed for immunity-related genes, hypothesized to be involved in cell recognition and adhesion, and for fluorescent protein genes. Principal component analysis of gene expression profiles resulted in separation between the different morphogenetic cues and exposure times, and not only identified those genes involved in the early response but also those which influenced downstream biological changes leading to larval metamorphosis or settlement. © 2014 Siboni et al.

Simpson, JL, Powell, H, Baines, KJ, Milne, D, Coxson, HO, Hansbro, PM & Gibson, PG 2014, 'The Effect of Azithromycin in Adults with Stable Neutrophilic COPD: A Double Blind Randomised, Placebo Controlled Trial', PLoS ONE, vol. 9, no. 8, pp. e105609-e105609.
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Background: Chronic Obstructive Pulmonary Disease (COPD) is a progressive airway disease characterised by neutrophilic airway inflammation or bronchitis. Neutrophilic bronchitis is associated with both bacterial colonisation and lung function decline and is common in exacerbations of COPD. Despite current available therapies to control inflammation, neutrophilic bronchitis remains common. This study tested the hypothesis that azithromycin treatment, as an add-on to standard medication, would significantly reduce airway neutrophil and neutrophils chemokine (CXCL8) levels, as well as bacterial load. We conducted a randomised, double-blind, placebo-controlled study in COPD participants with stable neutrophilic bronchitis. Methods: Eligible participants (n = 30) were randomised to azithromycin 250 mg daily or placebo for 12 weeks in addition to their standard respiratory medications. Sputum was induced at screening, randomisation and monthly for a 12 week treatment period and processed for differential cell counts, CXCL8 and neutrophil elastase assessment. Quantitative bacteriology was assessed in sputum samples at randomisation and the end of treatment visit. Severe exacerbations where symptoms increased requiring unscheduled treatment were recorded during the 12 week treatment period and for 14 weeks following treatment. A sub-group of participants underwent chest computed tomography scans (n = 15). Results: Nine participants with neutrophilic bronchitis had a potentially pathogenic bacteria isolated and the median total bacterial load of all participants was 5.22×107 cfu/mL. Azithromycin treatment resulted in a non-significant reduction in sputum neutrophil proportion, CXCL8 levels and bacterial load. The mean severe exacerbation rate was 0.33 per person per 26 weeks in the azithromycin group compared to 0.93 exacerbations per person in the placebo group (incidence rate ratio (95%CI): 0.37 (0.11,1.21), p = 0.062). For participants who underwent chest CT ...

Sinutok, S, Hill, R, Kuhl, M, Doblin, MA & Ralph, PJ 2014, 'Ocean acidification and warming alter photosynthesis and calcification of the symbiont-bearing foraminifera Marginopora vertebralis', MARINE BIOLOGY, vol. 161, no. 9, pp. 2143-2154.
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Slobozhanyuk, AP, Kapitanova, PV, Filonov, DS, Powell, DA, Shadrivov, IV, Lapine, M, Belov, PA, McPhedran, RC & Kivshar, YS 2014, 'Nonlinear interaction of meta-atoms through optical coupling', APPLIED PHYSICS LETTERS, vol. 104, no. 1, pp. 1-5.
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We propose and experimentally demonstrate a multi-frequency nonlinear coupling mechanism between split-ring resonators. We engineer the coupling between two microwave resonators through optical interaction, whilst suppressing the direct electromagnetic coupling. This allows for a power-dependent interaction between the otherwise independent resonators, opening interesting opportunities to address applications in signal processing, filtering, directional coupling, and electromagnetic compatibility. © 2014 AIP Publishing LLC.

Smith, MJA, Meylan, MH, McPhedran, RC & Poulton, CG 2014, 'A short remark on the band structure of free-edge platonic crystals', Waves in Random and Complex Media, vol. 24, no. 4, pp. 421-430.
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Sobinoff, AP, Sutherland, JM, Beckett, EL, Stanger, SJ, Johnson, R, Jarnicki, AG, McCluskey, A, St John, JC, Hansbro, PM & McLaughlin, EA 2014, 'Damaging legacy: maternal cigarette smoking has long-term consequences for male offspring fertility', Human Reproduction, vol. 29, no. 12, pp. 2719-2735.
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Study question

What are the effects on fertility of cigarette smoke-induced toxicity on male offspring exposed during the gestational/weaning period?

Summary answer

Maternal cigarette smoke exposure during the gestational/weaning period causes long-term defects in male offspring fertility.

What is known already

Cigarette smoke is a well-known reproductive toxicant which is particularly harmful to both fetal and neonatal germ cells. However, recent studies suggest a significant portion of young mothers in the developed world still smoke during pregnancy. In the context of male reproductive health, our understanding of the effects of in utero exposure on offspring fertility is limited.

Study design, size, duration

In this study, 27 C57BL/6 5-week-old female mice were exposed via the nose-only to cigarette smoke (treatment) or 27 were exposed to room air (control) for 6 weeks before being housed with stud males to produce litters. In the treatment group, smoke exposure continued throughout mating, pregnancy and lactation until weaning of pups at 21 days post birth. Male offspring were examined at post-natal days 3, 6, 12, 21 and 98 (adult).

Participants/materials, setting, methods

Approximately 108 maternal smoke-exposed C57BL/6 offspring and controls were examined. Spermatogenesis was examined using testicular histology and apoptosis/DNA damage was assessed using caspase immunohistochemistry and TUNEL. Sertoli cell morphology and fluctuations in the spermatogonial stem cell population were also examined using immunohistochemistry. Microarray and QPCR analysis were performed on adult testes to examine specific long-term transcriptomic alteration as a consequence of maternal smoke exposure. Sperm counts and motility, zona/oolemma binding assays, COMET analysis and mitochondrial genomic sequencing were also performed on spermatozoa obtained from adult treated and control mice. Fertility trials using exposed adult male offs...

Söderström, B, Skoog, K, Blom, H, Weiss, DS, von Heijne, G & Daley, DO 2014, 'Disassembly of the divisome in Escherichia coli: evidence that FtsZ dissociates before compartmentalization', Molecular Microbiology, vol. 92, no. 1, pp. 1-9.
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SummaryIn most bacteria cell division is mediated by a protein super‐complex called the divisome that co‐ordinates the constriction and scission of the cell envelope. FtsZ is the first of the divisome proteins to accumulate at the division site and is widely thought to function as a force generator that constricts the cell envelope. In this study we have used a combination of confocal fluorescence microscopy and fluorescence recovery after photobleaching (FRAP) to determine if divisome proteins are present at the septum at the time of cytoplasmic compartmentalization in Escherichia coli. Our data suggest that many are, but that FtsZ and ZapA disassemble before the cytoplasm is sealed by constriction of the inner membrane. This observation implies that FtsZ cannot be a force generator during the final stage(s) of envelope constriction in E. coli.

Solntsev, AS, Setzpfandt, F, Clark, AS, Wu, CW, Collins, MJ, Xiong, C, Schreiber, A, Katzschmann, F, Eilenberger, F, Schiek, R, Sohler, W, Mitchell, A, Silberhorn, C, Eggleton, BJ, Pertsch, T, Sukhorukov, AA, Neshev, DN & Kivshar, YS 2014, 'Generation of Nonclassical Biphoton States through Cascaded Quantum Walks on a Nonlinear Chip', Physical Review X, vol. 4, no. 3.
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Song, G, Liu, L, Han, J, Wang, C & Wang, G 2014, 'Polypyrrole single and double-shelled nanospheres templated by pyrrole–Hg(II) complex: Synthesis, characterization, formation mechanism and electrochemical performance', Synthetic Metals, vol. 197, pp. 126-133.
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© 2014 Elsevier B.V. All rights reserved. Spherical and yolk/shell nanostructures of pyrrole (Py)-Hg(II) complex have been formed by mixing Py monomer with HgCl2 in aqueous solution as white precipitation. Templated by spherical and yolk/shell nanostructures of Py-Hg(II) complex, polypyrrole (PPy) single and double-shelled hollow nanospheres have been successfully fabricated by simply introducing an oxidant to initial the polymerization of Py monomer on the surface of templates. Formation mechanisms of PPy nanostructures involved have been discussed in detail according to experimental observations. When hollow PPy spheres were used as the electrode materials for the supercapacitors, the specific capacity can achieve 252 F g-1 at the current density of 0.5 A g-1. Results indicated that the material has good cyclic stability, and is suitable to be applied as a good supercapacitor material.

Speer, M 2014, 'Conceptual Models of Severe Flash Flood Producing Rain in Two Distinct New South Wales Locations.', Centre for Australian Weather and Climate Research Research Letters, no. 11.

Spicer, T, Fernandez-Vega, V, Chase, P, Scampavia, L, To, J, Dalton, JP, Da Silva, FL, Skinner-Adams, TS, Gardiner, DL, Trenholme, KR, Brown, CL, Ghosh, P, Porubsky, P, Wang, JL, Whipple, DA, Schoenen, FJ & Hodder, P 2014, 'Identification of Potent and Selective Inhibitors of the Plasmodium falciparum M18 Aspartyl Aminopeptidase (PfM18AAP) of Human Malaria via High-Throughput Screening', SLAS Discovery, vol. 19, no. 7, pp. 1107-1115.
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The target of this study, the PfM18 aspartyl aminopeptidase (PfM18AAP), is the only AAP present in the genome of the malaria parasite Plasmodium falciparum. PfM18AAP is a metallo-exopeptidase that exclusively cleaves N-terminal acidic amino acids glutamate and aspartate. It is expressed in parasite cytoplasm and may function in concert with other aminopeptidases in protein degradation, of, for example, hemoglobin. Previous antisense knockdown experiments identified a lethal phenotype associated with PfM18AAP, suggesting that it is a valid target for new antimalaria therapies. To identify inhibitors of PfM18AAP function, a fluorescence enzymatic assay was developed using recombinant PfM18AAP enzyme and a fluorogenic peptide substrate (H-Glu-NHMec). This was screened against the Molecular Libraries Probe Production Centers Network collection of ∼292,000 compounds (the Molecular Libraries Small Molecule Repository). A cathepsin L1 (CTSL1) enzyme-based assay was developed and used as a counterscreen to identify compounds with nonspecific activity. Enzymology and phenotypic assays were used to determine mechanism of action and efficacy of selective and potent compounds identified from high-throughput screening. Two structurally related compounds, CID 6852389 and CID 23724194, yielded micromolar potency and were inactive in CTSL1 titration experiments (IC50 >59.6 μM). As measured by the Ki assay, both compounds demonstrated micromolar noncompetitive inhibition in the PfM18AAP enzyme assay. Both CID 6852389 and CID 23724194 demonstrated potency in malaria growth assays (IC50 4 μM and 1.3 μM, respectively). © 2014 Society for Laboratory Automation and Screening.

Stark, D, Barratt, JLN, Roberts, T, Marriott, D, Harkness, JT & Ellis, J 2014, 'Activity of benzimidazoles against Dientamoeba fragilis (Trichomonadida, Monocercomonadidae) in vitro and correlation of beta-tubulin sequences as an indicator of resistance', PARASITE, vol. 21.
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Recently, Dientamoeba fragilis has emerged as a significant and common enteropathogen. The majority of patients with dientamoebiasis present with gastrointestinal complaints and chronic symptoms are common. Numerous studies have successfully demonstrated parasite clearance, coupled with complete resolution of clinical symptoms following treatment with various antiparasitic compounds. Despite this, there is very little in vitro susceptibility data available for the organism. Benzimidazoles are a class of antiparasitic drugs that are commonly used for the treatment of protozoan and helminthic infections. Susceptibility testing was undertaken on four D. fragilis clinical isolates against the following benzimidazoles: albendazole, flubendazole, mebendazole, nocodazole, triclabendazole and thiabendazole. The activities of the antiprotozoal compounds at concentrations ranging from 2 μg/mL to 500 μg/mL were determined via cell counts of D. fragilis grown in xenic culture. All tested drugs showed no efficacy. The beta-tubulin transcript was sequenced from two of the D. fragilis isolates and amino acid sequences predicted a susceptibility to benzimidazoles. This is the first study to report susceptibility profiles for benzimidazoles against D. fragilis, all of which were not active against the organism. This study also found that beta-tubulin sequences cannot be used as a reliable marker for resistance of benzimidazoles in D. fragilis. © D. Stark et al., published by EDP Sciences, 2014.

Stark, D, Garcia, LS, Barratt, JLN, Phillips, O, Roberts, T, Marriott, D, Harkness, J & Ellis, JT 2014, 'Description of Dientamoeba fragilis Cyst and Precystic Forms from Human Samples', JOURNAL OF CLINICAL MICROBIOLOGY, vol. 52, no. 7, pp. 2680-2683.
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Dientamoeba fragilis is a common enteropathogen of humans. Recently a cyst stage of the parasite was described in an animal model; however, no cyst stage has been described in detail from clinical samples. We describe both cyst and precystic forms from human clinical samples. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Stark, D, Roberts, T, Ellis, JT, Marriott, D & Harkness, J 2014, 'Evaluation of the EasyScreen (TM) Enteric Parasite Detection Kit for the detection of Blastocystis spp., Cryptosporidium spp., Dientamoeba fragilis, Entamoeba complex, and Giardia intestinalis from clinical stool samples', DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE, vol. 78, no. 2, pp. 149-152.
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The aim of this study was to evaluate the EasyScreen Enteric Parasite Detection Kit (Genetic Signatures, Sydney, Australia) for the detection and identification of 5 common enteric parasites: Blastocystis spp., Cryptosporidium spp., Dientamoeba fragilis, Entamoeba complex, and Giardia intestinalis in human clinical samples. A total of 358 faecal samples were included in the study. When compared to real-time PCR and microscopy, the EasyScreen Enteric Parasite Detection Kit exhibited 92-100% sensitivity and 100% specificity and detected all commonly found genotypes and subtypes of clinically important human parasites. No cross reactivity was detected in stool samples containing various other bacterial, viral, and/or protozoan species. The EasyScreen PCR assay was able to provide rapid, sensitive, and specific simultaneous detection and identification of the 5 most important diarrhoea-causing enteric parasites that infect humans. It should be noted, however, that the EasyScreen Kit does not substitute for microscopy or for additional PCRs as it does not detect the pathogenic Coccidia spp. Cystoisospora belli or Cyclospora cayetanensis and it does not differentiate between pathogenic and nonpathogenic Entamoeba spp. This study also highlights the lack of sensitivity demonstrated by microscopy; as such, molecular methods should be considered the diagnostic method of choice for enteric parasites.

Starkey, MR, Nguyen, DH, Essilfie, AT, Kim, RY, Hatchwell, LM, Collison, AM, Yagita, H, Foster, PS, Horvat, JC, Mattes, J & Hansbro, PM 2014, 'Tumor necrosis factor-related apoptosis-inducing ligand translates neonatal respiratory infection into chronic lung disease', Mucosal Immunology, vol. 7, no. 3, pp. 478-488.
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Stojanovska, N, Kelly, T, Tahtouh, M, Beavis, A & Fu, S 2014, 'Analysis of amphetamine-type substances and piperazine analogues using desorption electrospray ionisation mass spectrometry', RAPID COMMUNICATIONS IN MASS SPECTROMETRY, vol. 28, no. 7, pp. 731-740.
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RATIONALE: Although amphetamine-type substances (ATS) have been investigated extensively in recent years, scarce data is available on screening tests for piperazine analogues. The need for a universal technique capable of detecting an extensive range of drug compounds becomes increasingly important with the continued emergence of novel drug analogues. METHODS: Desorption electrospray ionisation mass spectrometry (DESI-MS) is a technique that allows examination of compounds in drug materials directly from ambient surfaces. In this study, DESI-MS was utilised in the analysis of ATS including amphetamine (AP), methylamphetamine (MA), 3,4-methylenedioxymethylamphetamine (MDMA), N,N-dimethylamphetamine (DMA), 4-methoxyamphetamine (PMA) and 4-methoxymethylamphetamine (PMMA), and piperazine analogues including 1-benzylpiperazine (BZP), 1-[3-trifluoromethyl)phenyl]piperazine (TFMPP), 1-(3- chlorophenyl)piperazine (mCPP) and 1-(4-methoxyphenyl)piperazine (MeOPP). Semi-porous polytetrafluoroethylene (PTFE or Teflon) sheets welled with a 3 mm hole punch were used to contain the 2 µL liquid sample (spot size 7 mm2). RESULTS: The limits of detection (LODs) of these compounds using DESI-MS were determined to be in the range 0.022.80 µg/mm2. The intra-day and inter-day precision of the technique were <25% and <33%, respectively. DESI-MS was successful in determining the compound of interest and reaction by-products and impurities in the samples tested (such as 1,4-dibenzylpiperazine in BZP samples) with the exception of those present in trace amounts. The effects of common adulterants on the detectability of MA were evaluated. The addition of magnesium stearate to MA significantly enhanced the signal response. CONCLUSIONS: This work has demonstrated the applicability of DESI-MS in the screening and profiling of MDMA, PMMA, BZP, TFMPP, mCPP, MeOPP as well as other complex mixtures. Copyright © 2014 John Wiley & Sons, Ltd.

Stojanovska, N, Tahtouh, M, Kelly, T, Beavis, A & Fu, S 2014, 'Presumptive analysis of 4-methylmethcathinone (mephedrone) using Desorption Electrospray Ionisation - Mass Spectrometry (DESI-MS)', AUSTRALIAN JOURNAL OF FORENSIC SCIENCES, vol. 46, no. 4, pp. 411-423.
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4-Methylmethcathione (4-MMC or mephedrone) is a prevalent drug of abuse globally. 4-MMC is often marketed as `bath salts and is readily available over the internet. The need for a rapid universal technique capable of detecting an extensive range of drug compounds has become increasingly important with the continued emergence of novel drug analogues. Desorption electrospray ionisation - mass spectrometry (DESI-MS) is a mass spectrometry technique that allows for the analysis of compounds directly from ambient surfaces, reducing or eliminating the need for sample preparation. Although 4-MMC has gained significant attention in recent years, the application of the DESI-MS technique to the fast presumptive detection and chemical analysis of this analogue has not been presented. In the present study, DESI-MS was applied to the rapid qualitative analysis of 4-MMC. A particularly suitable surface, semi-porous polytetrafluoroethylene (PTFE, Teflon) was utilised, as it generated the least variable signal and reproducibility compared to other surfaces (polymethyl-methacrylate (PMMA) and polyvinyl chloride (PVC)). Selectivity of the technique to the detection of 4-MMC was evaluated by analysing a range of adulterated samples including mixtures containing caffeine, methylamphetamine, cathinone and paracetamol. Specificity based on tandem MS (MS/MS) was also demonstrated by analysing substances with the same molecular formula as 4-MMC. Accuracy (% RE) and precision (% RSD) of the method were found to be within 13% and 38%, respectively; and therefore the quantitative data provided by the DESI-MS method is limited compared to gas chromatography-mass spectrometry (GC-MS; accuracy < 13% and precision < 12%). The results suggest that DESI-MS can greatly aid in the rapid presumptive identification of 4-MMC and other similar novel drug analogues.

Sturmberg, BCP, Dossou, KB, Botten, LC, Asatryan, AA, Poulton, CG, McPhedran, RC & de Sterke, CM 2014, 'Optimizing Photovoltaic Charge Generation of Nanowire Arrays: A Simple Semi-Analytic Approach', ACS PHOTONICS, vol. 1, no. 8, pp. 683-689.
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Nanowire arrays exhibit efficient light coupling and strong light trapping, making them well suited to solar cell applications. The processes that contribute to their absorption are interrelated and highly dispersive, so the only current method of optimizing the absorption is by intensive numerical calculations. We present an efficient alternative that depends solely on the wavelength-dependent refractive indices of the constituent materials. We choose each array parameter such that the number of modes propagating away from the absorber is minimized, while the number of resonant modes within the absorber is maximized. From this we develop a semi-analytic method that quantitatively identifies the small range of parameters where arrays achieve maximum short-circuit currents. This provides a fast route to optimizing NW array cell efficiencies by greatly reducing the geometries to study with full device models. Our approach is general and applies to a variety of materials and to a large range of array thicknesses.

Su, D, Dou, S & Wang, G 2014, 'ChemInform Abstract: WS₂@graphene Nanocomposites as Anode Materials for Na‐Ion Batteries with Enhanced Electrochemical Performances.', ChemInform, vol. 45, no. 26, pp. no-no.
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AbstractWS2@graphene nanocomposites, in which WS2 nanocrystals are uniformly anchored on graphene nanosheets, are prepared by ultrasonication (30 min) of an aqueous suspension of WCl6 and freshly prepared graphite oxide nanosheets followed by hydrothermal treatment in the presence of cysteine (autoclave, 200 °C, 12 h).

Su, D, Dou, S & Wang, G 2014, 'Mesocrystal Co3O4 nanoplatelets as high capacity anode materials for Li-ion batteries', Nano Research, vol. 7, no. 5, pp. 794-803.
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Faceted crystals with exposed highly reactive planes have attracted intensive investigations for applications. Herein, we demonstrate a general synthetic method to prepare mesocrystal Co3O4 with predominantly exposed {111} reactive facets by the in situ thermal decomposition from Co(OH)2 nanoplatelets. The mesocrystal feature was identified by field emission scanning electron microscopy, transmission electron microscopy, selected area electron diffraction, and N2 isotherm analyses. When applied as anode material in lithium-ion batteries, mesocrystal Co3O4 nanoplatelets delivered a high specific capacity and an outstanding high rate performance. The superior electrochemical performance should be ascribed to the predominantly exposed {111} active facets and highly accessible surfaces. This synthetic strategy could be extended to prepare other mesocrystal functional nanomaterials. [Figure not available: see fulltext.] © 2014 Tsinghua University Press and Springer-Verlag Berlin Heidelberg.

Su, D, Dou, S & Wang, G 2014, 'Single Crystalline Co3O4 Nanocrystals Exposed with Different Crystal Planes for Li-O2 Batteries', Scientific Reports, vol. 4, no. 1.
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Single crystalline Co3O4 nanocrystals exposed with different crystal planes were synthesised, including cubic Co3O 4 nanocrystals enclosed by {100} crystal planes, pseudo octahedral Co3O4 enclosed by {100} and {110} crystal planes, Co 3O4 nanosheets exposed by {110} crystal planes, hexagonal Co3O4 nanoplatelets exposed with {111} crystal planes, and Co3O4 nanolaminar exposed with {112} crystal planes. Well single crystalline features of these Co3O4 nanocrystals were confirmed by FESEM and HRTEM analyses. The electrochemical performance for Li-o2 batteries shows that Co3O4 nanocrystals can significantly reduce the discharge-charge over-potential via the effect on the oxygen evolution reaction (OER). From the comparison on their catalytic performances, we found that the essential factor to promote the oxygen evolution reactions is the surface crystal planes of Co3O4 nanocrystals, namely, crystal planes-dependent process. The correlation between different Co3O4 crystal planes and their effect on reducing charge-discharge over-potential was established: {100} < {110} < {112} < {111}.

Su, D, Dou, S & Wang, G 2014, 'WS2@graphene nanocomposites as anode materials for Na-ion batteries with enhanced electrochemical performances', Chemical Communications, vol. 50, no. 32, pp. 4192-4192.
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WS2@graphene nanocomposites were synthesized by a hydrothermal approach. When applied as anodes in Na-ion batteries, the WS 2@graphene nanocomposite exhibited a high reversible sodium storage capacity of about 590 mA h g-1. It also demonstrated excellent high rate performance and cyclability. © the Partner Organisations 2014.

Su, D, Xie, X & Wang, G 2014, 'Hierarchical Mesoporous SnO Microspheres as High Capacity Anode Materials for Sodium‐Ion Batteries', Chemistry – A European Journal, vol. 20, no. 11, pp. 3192-3197.
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AbstractMesoporous SnO microspheres were synthesised by a hydrothermal method using NaSO4 as the morphology directing agent. Field emission scanning electron microscopy (FESEM), transmission electron microscopy (TEM) and high‐resolution transmission electron microscopy (HRTEM) analyses showed that SnO microspheres consist of nanosheets with a thickness of about 20 nm. Each nanosheet contains a mesoporous structure with a pore size of approximately 5 nm. When applied as anode materials in Na‐ion batteries, SnO microspheres exhibited high reversible sodium storage capacity, good cyclability and a satisfactory high rate performance. Through ex situ XRD analysis, it was found that Na+ ions first insert themselves into SnO crystals, and then react with SnO to generate crystalline Sn, followed by Na–Sn alloying with the formation of crystalline NaSn2 phase. During the charge process, there are two slopes corresponding to the de‐alloying of Na–Sn compounds and oxidisation of Sn, respectively. The high sodium storage capacity and good electrochemical performance could be ascribed to the unique hierarchical mesoporous architecture of SnO microspheres.

Su, D, Xie, X, Dou, S & Wang, G 2014, 'CuO single crystal with exposed {001} facets - A highly efficient material for gas sensing and Li-ion battery applications', Scientific Reports, vol. 4, no. 1.
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Single crystal copper oxide nanoplatelets with a high percentage of {001} facets were synthesized by a facile hydrothermal approach. The as-prepared materials were characterized by X-ray diffraction, Fourier transform infrared spectroscopy, field emission scanning electron microscopy, and high resolution transmission microscopy. Via density functional theory calculations, it was found that the {001} facets are active crystal planes. When the single crystal CuO nanoplatelets were applied as an anode material in Li-ion batteries, they demonstrated outstanding electrochemical performance with high lithium storage capacity, satisfactory cyclability, and excellent high rate capacity. When used as a sensing material in gas sensors, they exhibited a superior sensitivity towards toxic and flammable gases.

Su, D, Xie, X, Munroe, P, Dou, S & Wang, G 2014, 'Mesoporous hexagonal Co3O4 for high performance lithium ion batteries', Scientific Reports, vol. 4, no. 1.
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© 2014 Macmillan Publishers Limited. Mesoporous Co3O4 nanoplates were successfully prepared by the conversion of hexagonal β-Co(OH) 2 nanoplates. TEM, HRTEM and N2 sorption analysis confirmed the facet crystal structure and inner mesoporous architecture. When applied as anode materials for lithium storage in lithium ion batteries, mesoporous Co3O4 nanocrystals delivered a high specific capacity. At 10 C current rate, as-prepared mesoporous Co3O4 nanoplates delivered a specific capacity of 1203 mAh/g at first cycle and after 200 cycles it can still maintain a satisfied value (330 mAh/g). From ex-situ TEM, SAED and FESEM observation, it was found that mesoporous Co3O4 nanoplates were reduced to Li2O and Co during the discharge process and re-oxidised without losing the mesoporous structure during charge process. Even after 100 cycles, mesoporous Co3O4 crystals still preserved their pristine hexagonal shape and mesoporous nanostructure.

Su, DW, Dou, SX & Wang, GX 2014, 'Hierarchical orthorhombic V2O5 hollow nanospheres as high performance cathode materials for sodium-ion batteries', JOURNAL OF MATERIALS CHEMISTRY A, vol. 2, no. 29, pp. 11185-11194.
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Vanadyl ethylene glycolate hollow hierarchical nanospheres were synthesized via a template-free polyolinduced solvothermal process. After sintering, vanadium pentoxide (V2O5) with well-preserved spherical structures was obtained. Refined X-ray diffraction and transmission electron microscopy analyses identified that the V2O5 hollow nanospheres were constructed from hierarchical nanocrystals with predominantly exposed {110} crystal planes. When applied as cathode materials for sodium-ion batteries (Na-ion batteries), the V2O5 hollow nanospheres delivered a specific discharge capacity of ~150 mA h g-1, which is equal to one Na+ ion insertion per V2O5 formula unit. Theoretical modelling on the volume expansion and stress evolution on Na+ ion insertion revealed that the prolonged cycling stability could be ascribed to the porous hollow spherical architecture. Furthermore, the exposed {110} facets of V2O5 nanocrystals with two-dimensional diffusion paths for Na+ ion intercalation also contribute to high rate capacity and excellent cycling performance.

Sukhorukov, AA, Solntsev, AS, Kruk, SS, Neshev, DN & Kivshar, YS 2014, 'Nonlinear coupled-mode theory for periodic plasmonic waveguides and metamaterials with loss and gain', Optics Letters, vol. 39, no. 3, pp. 462-462.
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Sun, B, Huang, X, Chen, S, Munroe, P & Wang, G 2014, 'Porous Graphene Nanoarchitectures: An Efficient Catalyst for Low Charge-Overpotential, Long Life, and High Capacity Lithium-Oxygen Batteries', NANO LETTERS, vol. 14, no. 6, pp. 3145-3152.
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The electrochemical performance of lithium-oxygen (Li-O2) batteries awaits dramatic improvement in the design of porous cathode electrodes with sufficient spaces to accommodate the discharge products and discovery of effective cathode catalysts to promote both oxygen reduction reactions and oxygen evolution reactions. Herein, we report the synthesis of porous graphene with different pore size architectures as cathode catalysts for Li-O2 batteries. Porous graphene materials exhibited significantly higher discharge capacities than that of nonporous graphene. Furthermore, porous graphene with pore diameter around 250 nm showed the highest discharge capacity among the porous graphene with the small pores (about 60 nm) and large pores (about 400 nm). Moreover, we discovered that addition of ruthenium (Ru) nanocrystals to porous graphene promotes the oxygen evolution reaction. The Ru nanocrystal-decorated porous graphene exhibited an excellent catalytic activity as cathodes in Li-O2 batteries with a high reversible capacity of 17 700 mA h g-1, a low charge/discharge overpotential (about 0.355 V), and a long cycle life up to 200 cycles (under the curtaining capacity of 1000 mAh g-1). The novel porous graphene architecture inspires the development of high-performance Li-O2 batteries. © 2014 American Chemical Society.

Sun, B, Huang, X, Chen, S, Zhang, J & Wang, G 2014, 'An optimized LiNO3/DMSO electrolyte for high-performance rechargeable Li-O-2 batteries', RSC ADVANCES, vol. 4, no. 22, pp. 11115-11120.
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Finding stable electrolytes is essential to address the poor cycling capability of current rechargeable non-aqueous Li-O2 batteries. An optimized dimethyl sulfoxide (DMSO) based electrolyte using lithium nitrate (LiNO3) as the lithium salt has been first investigated for rechargeable Li-O2 batteries. The charge over-potential of Li-O 2 batteries with LiNO3/DMSO electrolyte is 0.42 V lower than that of batteries with LiClO4/DMSO electrolyte. The Li-O 2 batteries with LiNO3/DMSO electrolyte also showed excellent high C-rate performance and good cycling stability. © 2014 The Royal Society of Chemistry.

Sun, B, Huang, X, Chen, S, Zhao, Y, Zhang, J, Munroe, P & Wang, G 2014, 'Hierarchical macroporous/mesoporous NiCo2O4 nanosheets as cathode catalysts for rechargeable Li-O-2 batteries', JOURNAL OF MATERIALS CHEMISTRY A, vol. 2, no. 30, pp. 12053-12059.
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The key factor to improve the electrochemical performance of Li-O 2 batteries is to find bi-functional cathode catalysts to promote the oxygen reduction and evolution reactions. Despite tremendous effects, developing cathode catalysts with high activity remains a great challenge. Herein, we report the synthesis of hierarchical macroporous/mesoporous NiCo 2O4 nanosheets as an effective cathode catalyst for Li-O2 batteries. The hierarchical porous catalyst was synthesized by a hydrothermal method, followed by low temperature calcination. SEM and TEM observations clearly present that the as-prepared NiCo2O4 nanosheets showed a hierarchical porous structure with mesopores distributed through the surface of NiCo2O4 nanosheets and macropores formed between the crumpled nanosheets. When investigating as the cathode catalyst in Li-O2 batteries, the as-prepared NiCo2O 4 nanosheets exhibited higher reversible capacity, lower charge/discharge overpotential, and better cycling stability than those of pristine carbon black. The enhanced electrochemical performance of NiCo 2O4 nanosheets should be attributed not only to the high catalytic activity of NiCo2O4 towards oxygen reduction reaction and oxygen evolution reaction, but also to the novel hierarchical porous structure of NiCo2O4. This journal is © the Partner Organisations 2014.

Sun, H-T, Zhou, J & Qiu, J 2014, 'Recent advances in bismuth activated photonic materials', Progress in Materials Science, vol. 64, pp. 1-72.
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Bismuth is one of the most thoroughly investigated main group elements, which has been regarded as ‘the wonder metal’ because of its diverse oxidation states and profound propensities to form bismuth clusters, resulting from the easy involvement in chemical combinations for the electrons in the p orbital. This peculiarity allows them to behave as smart optically active centers in diverse host materials. Remarkable progress in the research of bismuth activated photonic materials has been seen over the last ten years owing to their unique properties and important applications in areas of telecommunication, biomedicine, white light illumination and lasers. The aim of this review is to present a critical overview of the current state of the art in bismuth activated photonic materials, their features, advantages and limitations as well as the future research trends. We first shortly introduce the fundamental properties of bismuth element including principles of bismuth-related luminescence and characterization techniques available. This is followed by a detailed discussion on the recent progress in the synthesis and characterization of bismuth-activated photonic materials, with an emphasis on material systems emitting in the near-infrared (NIR) spectral region. Furthermore, we describe the representative achievements regarding their prospective applications in broadband NIR optical amplifiers, fiber lasers, bioimaging, and white light-emitting diodes. Finally, we point out what key scientific questions remain to be answered, and present our perspectives on future research trends in this exciting field of sciences.

Sun, K, Eriksson, SE, Tan, Y, Zhang, L, Arnér, ESJ & Zhang, J 2014, 'Serum thioredoxin reductase levels increase in response to chemically induced acute liver injury', Biochimica et Biophysica Acta (BBA) - General Subjects, vol. 1840, no. 7, pp. 2105-2111.
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Supansomboon, S, Porkovich, A, Dowd, A, Arnold, MD & Cortie, MB 2014, 'Effect of Precursor Stoichiometry on the Morphology of Nanoporous Platinum Sponges', ACS APPLIED MATERIALS & INTERFACES, vol. 6, no. 12, pp. 9411-9417.
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Suwarno, SR, Chen, X, Chong, TH, McDougald, D, Cohen, Y, Rice, SA & Fane, AG 2014, 'Biofouling in reverse osmosis processes: The roles of flux, crossflow velocity and concentration polarization in biofilm development', Journal of Membrane Science, vol. 467, pp. 116-125.
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Biofilm development in a spacer-filled reverse osmosis membrane channel can influence both trans-membrane pressure (TMP) and channel pressure drop (δPCH). While current pretreatment methods are unable to completely tackle the biofouling problem, more insights are required to provide strategies to minimize the problem. This study examined the role of operating parameters (i.e. flux and crossflow velocity) to minimize biofouling in RO processes. The experiments were conducted with a lab-scale high pressure flat sheet RO reactor where changes in pressure drop along the channel and across the membrane were measured. The impact of biofouling was measured at constant fluxes, where the TMP rise and δPCH rise and the biofoulant was quantified as biovolumes of live and dead bacteria on autopsied membrane and spacer samples by confocal laser scanning microscopy (CLSM).The results show that TMP rise increased exponentially with increasing flux, and decreased with increasing crossflow velocity. The channel pressure drop, δPCH, increased when either flux or crossflow velocity was increased, and was more dependent on crossflow. The biofoulant volume on the membrane increased with flux and was less dependent on crossflow. The biofoulant associated with the spacer was much less than on the membrane and relatively insensitive to flux or crossflow velocity.The TMP rise could be correlated with the estimated concentration of nutrient at the membrane surface, Cw,N, highlighting the combined roles of flux and crossflow velocity in solute concentration polarization. Previous TMP rise data could also be correlated to the estimated Cw,N values. This observation suggests a biofouling mitigation strategy by controlling both incoming nutrient concentration and operating conditions (flux and crossflow). © 2014 Elsevier B.V.

Szabo, M, Parker, K, Guruprasad, S, Kuzhiumparambil, U, Lilley, RM, Tamburic, B, Schliep, M, Larkum, AWD, Schreiber, U, Raven, JA & Ralph, PJ 2014, 'Photosynthetic acclimation of Nannochloropsis oculata investigated by multi-wavelength chlorophyll fluorescence analysis', BIORESOURCE TECHNOLOGY, vol. 167, pp. 521-529.
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Multi-wavelength chlorophyll fluorescence analysis was utilised to examine the photosynthetic efficiency of the biofuel-producing alga Nannochloropsis oculata, grown under two light regimes; low (LL) and high (HL) irradiance levels. Wavelength dependency was evident in the functional absorption cross-section of Photosystem II (σII(λ)), absolute electron transfer rates (ETR(II)), and non-photochemical quenching (NPQ) of chlorophyll fluorescence in both HL and LL cells. While σII(λ) was not significantly different between the two growth conditions, HL cells upregulated ETR(II) 1.6-1.8-fold compared to LL cells, most significantly in the wavelength range of 440-540nm. This indicates preferential utilisation of blue-green light, a highly relevant spectral region for visible light in algal pond conditions. Under these conditions, the HL cells accumulated saturated fatty acids, whereas polyunsaturated fatty acids were more abundant in LL cells. This knowledge is of importance for the use of N. oculata for fatty acid production in the biofuel industry. © 2014 Elsevier Ltd.

Szabo, M, Wangpraseurt, D, Tamburic, B, Larkum, AWD, Schreiber, U, Suggett, DJ, Kuehl, M & Ralph, PJ 2014, 'Effective light absorption and absolute electron transport rates in the coral Pocillopora damicornis', PLANT PHYSIOLOGY AND BIOCHEMISTRY, vol. 83, pp. 159-167.
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Pulse Amplitude Modulation (PAM) fluorometry has been widely used to estimate the relative photosynthetic efficiency of corals. However, both the optical properties of intact corals as well as past technical constrains to PAM fluorometers have prevented calculations of the electron turnover rate of PSII. We used a new Multi-colour PAM (MC-PAM) in parallel with light microsensors to determine for the first time the wavelength-specific effective absorption cross-section of PSII photochemistry, σII(λ), and thus PAM-based absolute electron transport rates of the coral photosymbiont Symbiodinium both in culture and in hospite in the coral Pocillopora damicornis. In both cases, σII of Symbiodinium was highest in the blue spectral region and showed a progressive decrease towards red wavelengths. Absolute values for σII at 440nm were up to 1.5-times higher in culture than in hospite. Scalar irradiance within the living coral tissue was reduced by 20% in the blue when compared to the incident downwelling irradiance. Absolute electron transport rates of P.damicornis at 440nm revealed a maximum PSII turnover rate of ca. 250 electrons PSII-1 s-1, consistent with one PSII turnover for every 4 photons absorbed by PSII; this likely reflects the limiting steps in electron transfer between PSII and PSI. Our results show that optical properties of the coral host strongly affect light use efficiency of Symbiodinium. Therefore, relative electron transport rates do not reflect the productivity rates (or indeed how the photosynthesis-light response is parameterised). Here we provide a non-invasive approach to estimate absolute electron transport rates in corals. © 2014 Elsevier Masson SAS.

Tacchi, JL, Raymond, BBA, Jarocki, VM, Berry, IJ, Padula, MP & Djordjevic, SP 2014, 'Cilium Adhesin P216 (MHJ_0493) Is a Target of Ectodomain Shedding and Aminopeptidase Activity on the Surface of Mycoplasma hyopneumoniae', Journal of Proteome Research, vol. 13, no. 6, pp. 2920-2930.
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MHJ-0493 (P216) is a highly expressed cilium adhesin in Mycoplasma hyopneumoniae. P216 undergoes cleavage at position 1074 in the S/T-X-F↓-X-D/E-like motif 1072T-N-F↓Q-E1076 generating N-terminal and C-terminal fragments of 120 kDa (P120) and 85 kDa (P85) on the surface of M. hyopneumoniae. Here we show that several S/T-X-F↓X-D/E-like motifs exist in P216 but only 1072T-N- F↓Q-E1076 and 1344I-T-F↓A-D-Y1349 were determined to be bona fide processing sites by identifying semitryptic peptides consistent with cleavage at the phenylalanine residue. The location of S/T-X-F↓-X-D/E-like motifs within or abutting regions of protein disorder greater than 40 consecutive amino acids is consistent with our hypothesis that site access influences the cleavage efficiency. Approximately 20 cleavage fragments of P216 were identified on the surface of M. hyopneumoniae by LC-MS/MS analysis of biotinylated proteins and 2D SDS-PAGE. LC-MS/MS analysis of semitryptic peptides within P216 identified novel cleavage sites. Moreover, detection of a series of overlapping semitryptic peptides that differed by the loss a single amino acid at their N-terminus is consistent with aminopeptidase activity on the surface of M. hyopneumoniae. P120 and P85 and their cleavage fragments bind heparin and cell-surface proteins derived from porcine epithelial-like cells, indicating that P216 cleavage fragments retain the ability to bind glycosaminoglycans. © 2014 American Chemical Society.

Tahir, M, Cao, C, Butt, FK, Butt, S, Idrees, F, Ali, Z, Aslam, I, Tanveer, M, Mahmood, A & Mahmood, N 2014, 'Large scale production of novel g-C3N4 micro strings with high surface area and versatile photodegradation ability', CrystEngComm, vol. 16, no. 9, pp. 1825-1825.
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Tahir, M, Cao, C, Mahmood, N, Butt, FK, Mahmood, A, Idrees, F, Hussain, S, Tanveer, M, Ali, Z & Aslam, I 2014, 'Multifunctional g-C₃N₄ Nanofibers: A Template-Free Fabrication and Enhanced Optical, Electrochemical, and Photocatalyst Properties', ACS Applied Materials & Interfaces, vol. 6, no. 2, pp. 1258-1265.
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Tamburic, B, Guruprasad, S, Radford, DT, Szabo, M, Lilley, RM, Larkum, AWD, Franklin, JB, Kramer, DM, Blackburn, SI, Raven, JA, Schliep, M & Ralph, PJ 2014, 'The Effect of Diel Temperature and Light Cycles on the Growth of Nannochloropsis oculata in a Photobioreactor Matrix', PLOS ONE, vol. 9, no. 1, p. e86047.
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A matrix of photobioreactors integrated with metabolic sensors was used to examine the combined impact of light and temperature variations on the growth and physiology of the biofuel candidate microalgal species Nannochloropsis oculata. The experiments were performed with algal cultures maintained at a constant 20u C versus a 15°C to 25°C diel temperature cycle, where light intensity also followed a diel cycle with a maximum irradiance of 1920 μmol photons m-2 s^-1. No differences in algal growth (Chlorophyll a) were found between the two environmental regimes; however, the metabolic processes responded differently throughout the day to the change in environmental conditions. The variable temperature treatment resulted in greater damage to photosystem II due to the combined effect of strong light and high temperature. Cellular functions responded differently to conditions before midday as opposed to the afternoon, leading to strong hysteresis in dissolved oxygen concentration, quantum yield of photosystem II and net photosynthesis. Overnight metabolism performed differently, probably as a result of the temperature impact on respiration. Our photobioreactor matrix has produced novel insights into the physiological response of Nannochloropsis oculata to simulated environmental conditions. This information can be used to predict the effectiveness of deploying Nannochloropsis oculata in similar field conditions for commercial biofuel production. © 2014 Tamburic et al.

Tamburic, B, Szabo, M, Tran, N-AT, Larkum, AWD, Suggett, DJ & Ralph, PJ 2014, 'Action spectra of oxygen production and chlorophyll a fluorescence in the green microalga Nannochloropsis oculata', BIORESOURCE TECHNOLOGY, vol. 169, pp. 320-327.
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The first complete action spectrum of oxygen evolution and chlorophyll a fluorescence was measured for the biofuel candidate alga Nannochloropsis oculata. A novel analytical procedure was used to generate a representative and reproducible action spectrum for microalgal cultures. The action spectrum was measured at 14 discrete wavelengths across the visible spectrum, at an equivalent photon flux density of 60μmolphotonsm-2s-1. Blue light (~414nm) was absorbed more efficiently and directed to photosystem II more effectively than red light (~679nm) at light intensities below the photosaturation limit. Conversion of absorbed photons into photosynthetic oxygen evolution was maximised at 625nm; however, this maximum is unstable since neighbouring wavelengths (646nm) resulted in the lowest photosystem II operating efficiency. Identifying the wavelength-dependence of photosynthesis has clear implications to optimising growth efficiency and hence important economic implications to the algal biofuels and bioproducts industries. © 2014 Elsevier Ltd.

Tan, CH, Koh, KS, Xie, C, Tay, M, Zhou, Y, Williams, R, Ng, WJ, Rice, SA & Kjelleberg, S 2014, 'The role of quorum sensing signalling in EPS production and the assembly of a sludge community into aerobic granules', The ISME Journal, vol. 8, no. 6, pp. 1186-1197.
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Abstract Quorum sensing (QS) signalling has been extensively studied in single species populations. However, the ecological role of QS in complex, multi-species communities, particularly in the context of community assembly, has neither been experimentally explored nor theoretically addressed. Here, we performed a long-term bioreactor ecology study to address the links between QS, organization and composition of complex microbial communities. The conversion of floccular biomass to highly structured granules was found to be non-random, but strongly and positively correlated with N-acyl-homoserine-lactone (AHL)-mediated QS. Specific AHLs were elevated up to 100-fold and were strongly associated with the initiation of granulation. Similarly, the levels of particular AHLs decreased markedly during the granular disintegration phase. Metadata analysis indicated that granulation was accompanied by changes in extracellular polymeric substance (EPS) production and AHL add-back studies also resulted in increased EPS synthesis. In contrast to the commonly reported nanomolar to micromolar signal concentrations in pure culture laboratory systems, QS signalling in the granulation ecosystem occurred at picomolar to nanomolar concentrations of AHLs. Given that low concentrations of AHLs quantified in this study were sufficient to activate AHL bioreporters in situ in complex granular communities, AHL mediated QS may be a common feature in many natural and engineered ecosystems, where it coordinates community behaviour.

Tanveer, M, Cao, C, Aslam, I, Ali, Z, Idrees, F, Khan, WS, Butt, FK, Tahir, M & Mahmood, A 2014, 'Facile Synthesis of CuS Nanostructures: Structural, Optical and Photocatalytic Properties', Science of Advanced Materials, vol. 6, no. 12, pp. 2694-2701.
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Taudte, RV, Beavis, A, Blanes, L, Cole, N, Doble, P & Roux, C 2014, 'Detection of Gunshot Residues Using Mass Spectrometry', BIOMED RESEARCH INTERNATIONAL, vol. 2014, pp. 1-16.
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In recent years, forensic scientists have become increasingly interested in the detection and interpretation of organic gunshot residues (OGSR) due to the increasing use of lead- and heavy metal-free ammunition. This has also been prompted by the identification of gunshot residue- (GSR-) like particles in environmental and occupational samples. Various techniques have been investigated for their ability to detect OGSR. Mass spectrometry (MS) coupled to a chromatographic system is a powerful tool due to its high selectivity and sensitivity. Further, modern MS instruments can detect and identify a number of explosives and additives which may require different ionization techniques. Finally, MS has been applied to the analysis of both OGSR and inorganic gunshot residue (IGSR), although the 'gold standard' for analysis is scanning electron microscopy with energy dispersive X-ray microscopy (SEM-EDX). This review presents an overview of the technical attributes of currently available MS and ionization techniques and their reported applications to GSR analysis. © 2014 Regina Verena Taudte et al.

Tekwe, CD, Carter, RL, Cullings, HM & Carroll, RJ 2014, 'Multiple indicators, multiple causes measurement error models', Statistics in Medicine, vol. 33, no. 25, pp. 4469-4481.
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Multiple indicators, multiple causes(MIMIC) models are often employed by researchers studying the effects of an unobservable latent variable on a set of outcomes, when causes of the latent variable are observed. There are times, however, when the causes of the latent variable are not observed because measurements of the causal variable are contaminated by measurement error. The objectives of this paper are as follows: (i) to develop a novel model by extending the classical linear MIMIC model to allow both Berkson and classical measurement errors, defining the MIMIC measurement error (MIMIC ME) model; (ii) to develop likelihood‐based estimation methods for the MIMIC ME model; and (iii) to apply the newly defined MIMIC ME model to atomic bomb survivor data to study the impact of dyslipidemia and radiation dose on the physical manifestations of dyslipidemia. As a by‐product of our work, we also obtain a data‐driven estimate of the variance of the classical measurement error associated with an estimate of the amount of radiation dose received by atomic bomb survivors at the time of their exposure. Copyright © 2014 John Wiley & Sons, Ltd.

Teng, Y, Zhou, J, khisro, SN, Zhou, S & Qiu, J 2014, 'Elemental redistribution behavior in tellurite glass induced by high repetition rate femtosecond laser irradiation', Journal of Alloys and Compounds, vol. 601, pp. 212-216.
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The success in the fabrication of micro-structures in glassy materials using femtosecond laser irradiation has proved its potential applications in the construction of three-dimensional micro-optical components or devices. In this paper, we report the elemental redistribution behavior in tellurite glass after the irradiation of high repetition rate femtosecond laser pulses. The relative glass composition remained unchanged while the glass density changed significantly, which is quite different from previously reported results about the high repetition rate femtosecond laser induced elemental redistribution in silicate glasses. The involved mechanism is discussed with the conclusion that the glass network structure plays the key role to determine the elemental redistribution. This observation not only helps to understand the interaction process of femtosecond laser with glassy materials, but also has potential applications in the fabrication of micro-optical devices.

Teng, Y, Zhou, J, Nasir Khisro, S, Zhou, S & Qiu, J 2014, 'Persistent luminescence of SrAl2O4: Eu2+, Dy3+, Cr3+ phosphors in the tissue transparency window', Materials Chemistry and Physics, vol. 147, no. 3, pp. 772-776.
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We report on the persistent luminescence of SrAl2O4: Eu2+, Cr3+ phosphor centered at 760 nm. The phosphor was prepared by sol-gel-combustion method. Persistent luminescence from Cr3+ lasted for hundreds of seconds, comparable to the long afterglow from Eu2+ ions in the visible region based on the continuous energy transfer from Eu2+ ions to Cr3+ ions. The introduction of Dy3+ ions into the phosphor further prolonged the afterglow time of Eu2+ and Cr3+ ions through the depth control of the charge traps. The optimum doping concentrations for Eu2+, Cr3+ and Dy3+ were 1%, 2% and 1.5%, respectively.

Teng, Y, Zhou, J, Sharafudeen, K, Zhou, S, Miura, K & Qiu, J 2014, 'Space-selective crystallization of glass induced by femtosecond laser irradiation', Journal of Non-Crystalline Solids, vol. 383, pp. 91-96.
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Transparent glasses imbedded with functional nanocrystals have attracted considerable interest and been studied widely in the past several decades, due to their applications in optical devices, such as optical amplifiers, nonlinear optical devices, optical storage, 3D displays, etc. Femtosecond (fs) laser irradiation induced crystallization of glass has been proved to be a powerful tool to realize the space-selective precipitation of various nanocrystals inside glasses. In this review, we highlight our recent research achievements on the fs laser induced precipitation of nanocrystals inside glasses, including nonlinear optical crystal, upconversion luminescence crystal, high refractive index crystal, and metal nanoparticles. These studies not only help to understand the interaction process between fs laser and glassy materials, but also have potential applications in the fabrication of micro-optical devices.

Thenkabail, PS, Gumma, MK, Teluguntla, P & Mohammed, IA 2014, 'HYPERSPECTRAL REMOTE SENSING OF VEGETATION AND AGRICULTURAL CROPS', PHOTOGRAMMETRIC ENGINEERING AND REMOTE SENSING, vol. 80, no. 8, pp. 697-709.

Thiruvady, D, Wallace, M, Gu, H & Schutt, A 2014, 'A lagrangian relaxation and ACO hybrid for resource constrained project scheduling with discounted cash flows', Journal of Heuristics, vol. 20, no. 6, pp. 643-676.
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Thwe, LM, Cantrill, LC, Catchpoole, DR, Lau, L & Byrne, JA 2014, 'Abstract B51: Extraction and analysis of genomic DNA from formalin-fixed paraffin-embedded neuroblastoma samples following laser capture microdissection', Cancer Research, vol. 74, no. 20_Supplement, pp. B51-B51.
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Abstract Introduction: Neuroblastoma (NB) is the most common extracranial solid tumor of infants. We constructed a tissue microarray (TMA) including 47 diagnostic NB cases and performed immunohistochemical (IHC) staining for a number of biomarkers. Differential IHC staining was identified between duplicate tissue cores for a proportion of NB cases. Differential IHC staining occurs frequently in cancer specimens, and can be due to technical factors, tissue artefacts, or underlying biological differences between tumor sub-regions. As laser capture microdissection (LCM) allows isolation of cells from formalin-fixed paraffin-embedded (FFPE) tissue slides, we applied LCM to FFPE NB samples, to investigate the basis of differential IHC staining. Material and Methods: NSE, NB84, ALK, TPD52 and MGMT proteins were detected within diagnostic NB TMA cores and whole NB sections using IHC. Cells were isolated from FFPE sections using LCM, and genomic DNA was extracted using the QIAamp DNA FFPE Tissue Kit. Extracted genomic DNA was quantified using a Nanodrop spectrophotometer, and DNA quality was assessed by a Bioanalyzer 2100. All DNA samples were tested using PCR with TPD52 and ALK primers. Results including clinical and sample variables were analysed using SPSS version 19. Results: Of 47 NB cases within the TMA, 35 cases were represented by duplicate tissue cores, whereas the remaining 12 cases were represented by single cores. IHC analysis of 5 biomarkers showed visually different IHC staining in tumour tissue between duplicate tissue cores in 15/35 (43%) cases. Whole tissue sections from 6 of these 15 cases were then examined, which reproduced differential IHC staining. Isolation of NB cells by LCM was successfully performed after substantial optimisation. A total of 14 regions from 8 NB cases were microdissected, producing DNA yields ranging from 0.1...

Tian, H, Zhang, XL, Scott, J, Ng, C & Amal, R 2014, 'TiO₂-supported copper nanoparticles prepared via ion exchange for photocatalytic hydrogen production', J. Mater. Chem. A, vol. 2, no. 18, pp. 6432-6438.
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Cu/TiO₂ synthesized through ion exchange provides finer, more highly dispersed metallic copper deposits, displaying a ∼44% greater hydrogen generation capacity than WI Cu/TiO₂ prepared using wet impregnation. The difference in activity was maintained over repeated reaction cycles.

Tong, W, Fox, K, Ganesan, K, Turnley, AM, Shimoni, O, Tran, PA, Lohrmann, A, McFarlane, T, Ahnood, A, Garrett, DJ, Meffin, H, O'Brien-Simpson, NM, Reynolds, EC & Prawer, S 2014, 'Fabrication of planarised conductively patterned diamond for bio-applications', Materials Science and Engineering: C, vol. 43, pp. 135-144.
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The development of smooth, featureless surfaces for biomedical microelectronics is a challenging feat. Other than the traditional electronic materials like silicon, few microelectronic circuits can be produced with conductive features without compromising the surface topography and/or biocompatibility. Diamond is fast becoming a highly sought after biomaterial for electrical stimulation, however, its inherent surface roughness introduced by the growth process limits its applications in electronic circuitry. In this study, we introduce a fabrication method for developing conductive features in an insulating diamond substrate whilst maintaining a planar topography. Using a combination of microwave plasma enhanced chemical vapour deposition, inductively coupled plasma reactive ion etching, secondary diamond growth and silicon wet-etching, we have produced a patterned substrate in which the surface roughness at the interface between the conducting and insulating diamond is approximately 3 nm. We also show that the patterned smooth topography is capable of neuronal cell adhesion and growth whilst restricting bacterial adhesion. © 2014 Elsevier B.V.

Ton-That, C, Lem, LLC, Phillips, MR, Reisdorffer, F, Mevellec, J, Nguyen, T-P, Nenstiel, C & Hoffmann, A 2014, 'Shallow carrier traps in hydrothermal ZnO crystals', NEW JOURNAL OF PHYSICS, vol. 16, pp. 1-14.
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Native and hydrogen-plasma induced shallow traps in hydrothermally grown ZnO crystals have been investigated by charge-based deep level transient spectroscopy, photoluminescence and cathodoluminescence microanalysis. The as-grown ZnO exhibits a trap state at 23 meV, while H-doped ZnO produced by plasma doping shows two levels at 22 meV and 11 meV below the conduction band. As-grown ZnO displays the expected thermal decay of bound excitons with increasing temperature from 7 K, while we observed an anomalous behaviour of the excitonic emission in H-doped ZnO, in which its intensity increases with increasing temperature in the range 140-300 K. Based on a multitude of optical results, a qualitative model is developed which explains the Y line structural defects, which act as an electron trap with an activation energy of 11 meV, being responsible for the anomalous temperature-dependent cathodoluminescence of H-doped ZnO. © 2014 IOP Publishing Ltd and Deutsche Physikalische Gesellschaft.

Torpy, FR, Irga, PJ & Burchett, MD 2014, 'Profiling indoor plants for the amelioration of high CO2 concentrations', URBAN FORESTRY & URBAN GREENING, vol. 13, no. 2, pp. 227-233.
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Research over the last three decades has shown that indoor plants can reduce most types of urban air pollutants, however there has been limited investigation of their capacity to mitigate elevated levels of CO2. This study profiled the CO2 removal potential of eight common indoor plant species, acclimatised to both indoor and glasshouse lighting levels, to develop baseline data to facilitate the development of indoor plant installations to improve indoor air quality by reducing excess CO2 concentrations. The results indicate that, with the appropriate choice of indoor plant species and a targeted increase in plant specific lighting, plantscape installations could be developed to remove a proportion of indoor CO2. Further horticultural research and development will be required to develop optimum systems for such installations, which could potentially reduce the load on ventilation systems. © 2013 Elsevier GmbH.

Torres, MA, Ritchie, RJ, Lilley, RMC, Grillet, C & Larkum, AWD 2014, 'Measurement of photosynthesis and photosynthetic efficiency in two diatoms', NEW ZEALAND JOURNAL OF BOTANY, vol. 52, no. 1, pp. 6-27.
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Toth, M 2014, 'Advances in gas-mediated electron beam-induced etching and related material processing techniques', Applied Physics A, vol. 117, no. 4, pp. 1623-1629.
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© 2014, Springer-Verlag Berlin Heidelberg. Electron beam-induced etching (EBIE) has traditionally been used for top-down, direct-write, chemical dry etching, and iterative editing of materials. The present article reviews recent advances in EBIE modeling and emerging applications, with an emphasis on use cases in which the approaches that have conventionally been used to realize EBIE are instead used for material analysis, surface functionalization, or bottom-up growth of nanostructured materials. Such applications are used to highlight the shortcomings of existing quantitative EBIE models and to identify physicochemical phenomena that must be accounted for in order to enable full exploitation and predictive modeling of EBIE and related electron beam fabrication techniques.

Toth, M, Zachreson, C & Aharonovich, I 2014, 'Role of recombination pathway competition in spatially resolved cathodoluminescence spectroscopy', Applied Physics Letters, vol. 105, no. 24, pp. 241112-241112.
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Cathodoluminescence (CL) analysis enables characterization of optoelectronic materials and devices with high spatial resolution. However, data interpretation is complicated by the competitive nature of the CL generation process. Specifically, spatially resolved CL profiles are affected by both CL center distributions, and by the unknown distributions of recombination centers that do not generate peaks in measured CL spectra. Here, we use depth-resolved CL to show that the contribution of the latter can be deduced and removed from spatially resolved CL data. The utility of this technique is demonstrated using CL depth profiles of color centers in diamond.

Tout, J, Jeffries, TC, Webster, NS, Stocker, R, Ralph, PJ & Seymour, JR 2014, 'Variability in Microbial Community Composition and Function Between Different Niches Within a Coral Reef', MICROBIAL ECOLOGY, vol. 67, no. 3, pp. 540-552.
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To explore how microbial community composition and function varies within a coral reef ecosystem, we performed metagenomic sequencing of seawater from four niches across Heron Island Reef, within the Great Barrier Reef. Metagenomes were sequenced from seawater samples associated with (1) the surface of the coral species Acropora palifera, (2) the surface of the coral species Acropora aspera, (3) the sandy substrate within the reef lagoon and (4) open water, outside of the reef crest. Microbial composition and metabolic function differed substantially between the four niches. The taxonomic profile showed a clear shift from an oligotroph-dominated community (e.g. SAR11, Prochlorococcus, Synechococcus) in the open water and sandy substrate niches, to a community characterised by an increased frequency of copiotrophic bacteria (e.g. Vibrio, Pseudoalteromonas, Alteromonas) in the coral seawater niches. The metabolic potential of the four microbial assemblages also displayed significant differences, with the open water and sandy substrate niches dominated by genes associated with core house-keeping processes such as amino acid, carbohydrate and protein metabolism as well as DNA and RNA synthesis and metabolism. In contrast, the coral surface seawater metagenomes had an enhanced frequency of genes associated with dynamic processes including motility and chemotaxis, regulation and cell signalling. These findings demonstrate that the composition and function of microbial communities are highly variable between niches within coral reef ecosystems and that coral reefs host heterogeneous microbial communities that are likely shaped by habitat structure, presence of animal hosts and local biogeochemical conditions.

Trevathan-Tackett, S, Macreadie, P, Ralph, P & Seymour, J 2014, 'Detachment and flow cytometric quantification of seagrass-associated bacteria', JOURNAL OF MICROBIOLOGICAL METHODS, vol. 102, pp. 23-25.
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A new protocol was developed to detach bacteria from seagrass tissue and subsequently enumerate cells using flow cytometry (FCM). A method involving addition of the surfactant Tween 80 and vortexing resulted in maximum detachment efficiency of seagrass attached bacteria, providing a robust protocol for precisely enumerating seagrass-associated bacteria with FCM. Using this approach we detected cell concentrations between 2.0 × 105 and 8.0 × 106 cells mg- 1 DW tissue.

Trimborn, S, Thoms, S, Petrou, K, Kranz, SA & Rost, B 2014, 'Photophysiological responses of Southern Ocean phytoplankton to changes in CO2 concentrations: Short-term versus acclimation effects', JOURNAL OF EXPERIMENTAL MARINE BIOLOGY AND ECOLOGY, vol. 451, pp. 44-54.
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The present study examines how different pCO2 acclimations affect the CO2- and light-dependence of photophysiological processes and O2 fluxes in four Southern Ocean (SO) key phytoplankton species. We grew Chaetoceros debilis (Cleve), Pseudo-nitzschia subcurvata (Hasle), Fragilariopsis kerguelensis (O'Meara) and Phaeocystis antarctica (Karsten) under low (160μatm) and high (1000μatm) pCO2. The CO2- and light-dependence of fluorescence parameters of photosystem II (PSII) were determined by means of a fluorescence induction relaxation system (FIRe). In all tested species, nonphotochemical quenching (NPQ) is the primary photoprotection strategy in response to short-term exposure to high light or low CO2 concentrations. In C. debilis and P. subcurvata, PSII connectivity (p) and functional absorption cross-sections of PSII in ambient light (σPSII') also contributed to photoprotection while changes in re-oxidation times of Qa acceptor (τQa) were more significant in F. kerguelensis. The latter was also the only species being responsive to high acclimation pCO2, as these cells had enhanced relative electron transport rates (rETRs) and σPSII' while τQa and p were reduced under short-term exposure to high irradiance. Low CO2-acclimated cells of F. kerguelensis and all pCO2 acclimations of C. debilis and P. subcurvata showed dynamic photoinhibition with increasing irradiance. To test for the role and presence of the Mehler reaction in C. debilis and P. subcurvata, the light-dependence of O2 fluxes was estimated using membrane inlet mass spectrometry (MIMS). Our results show that the Mehler reaction is absent in both species under the tested conditions. We also observed that dark respiration was strongly reduced under high pCO2 in C. debilis while it remained unaltered in P. subcurvata. Our study revealed species-specific differences in the photophysiological responses to pCO2, both on the acclimation as well as the short-term level. © 2013 The Authors.

Tse, N, Morsch, M, Ghazanfari, N, Cole, L, Visvanathan, A, Leamey, C & Phillips, WD 2014, 'The Neuromuscular Junction: Measuring Synapse Size, Fragmentation and Changes in Synaptic Protein Density Using Confocal Fluorescence Microscopy', Journal of Visualized Experiments, no. 94.
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Tu, Z, Teng, Y, Zhou, J, Zhou, S & Qiu, J 2014, 'Micro-modification of luminescence property in Ag+-doped phosphate glass using femtosecond laser irradiation', Journal of Non-Crystalline Solids, vol. 383, pp. 161-164.
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Localized micro-structure and luminescence property are modified in Ag+-doped phosphate glass with high repetition rate femtosecond laser pulses. Confocal fluorescence spectra show that the luminescence intensity due to fs-laser induced Ag0 gradually increases and then decreases with the decreasing distance from the center of the laser-affected zone. In the inner structure, the intensity ratio of two Raman bands at 708 cm− 1 and 1210 cm− 1 decreases with the more close to the center of the laser-affected zone. A possible mechanism is proposed to explain the observed phenomena.

Turnbull, L & Whitchurch, CB 2014, 'Motility Assay: Twitching Motility', Methods in Molecular Biology, vol. 1149, no. 1, pp. 73-86.
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© Springer Science+Business Media New York 2014 Twitching motility is a mode of solid surface translocation that occurs under humid conditions on semisolid or solid surfaces, is dependent on the presence of retractile type IV pili and is independent of the presence of a fl agellum. Surface translocation via twitching motility is powered by the extension and retraction of type IV pili and can manifest as a complex multicellular collective behavior that mediates the active expansion of colonies cultured on the surface of solidified nutrient media, and of interstitial colonies that are cultured at the interface between solidified nutrient media and an abiotic material such as the base of a petri dish or a glass coverslip. Here we describe two methods for assaying twitching motility mediated interstitial colony expansion in P. aeruginosa. The first method, the “Macroscopic Twitching Assay,” can be used to determine if a strain is capable of twitching motility mediated interstitial colony expansion and can also be used to quantitatively assess the infl uence of mutation or environmental signals on this process. The second method, the “Microscopic Twitching Assay,” can be used for detailed interrogation of the movements of individual cells or small groups of bacteria during twitching motility mediated colony expansion.

Turnbull, L, Strauss, MP, Liew, ATF, Monahan, LG, Whitchurch, CB & Harry, EJ 2014, 'Super-resolution Imaging of the Cytokinetic Z Ring in Live Bacteria Using Fast 3D-Structured Illumination Microscopy (f3D-SIM)', JOVE-JOURNAL OF VISUALIZED EXPERIMENTS, no. 91.
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© JoVE 2006-2014. All Rights Reserved. Imaging of biological samples using fluorescence microscopy has advanced substantially with new technologies to overcome the resolution barrier of the diffraction of light allowing super-resolution of live samples. There are currently three main types of super-resolution techniques – stimulated emission depletion (STED), single-molecule localization microscopy (including techniques such as PALM, STORM, and GDSIM), and structured illumination microscopy (SIM). While STED and single-molecule localization techniques show the largest increases in resolution, they have been slower to offer increased speeds of image acquisition. Three-dimensional SIM (3D-SIM) is a wide-field fluorescence microscopy technique that offers a number of advantages over both single-molecule localization and STED. Resolution is improved, with typical lateral and axial resolutions of 110 and 280 nm, respectively and depth of sampling of up to 30 µm from the coverslip, allowing for imaging of whole cells. Recent advancements (fast 3D-SIM) in the technology increasing the capture rate of raw images allows for fast capture of biological processes occurring in seconds, while significantly reducing photo-toxicity and photobleaching Here we describe the use of one such method to image bacterial cells harboring the fluorescently-labelled cytokinetic FtsZ protein to show how cells are analyzed and the type of unique information that this technique can provide.

Ueland, M, Breton, HA & Forbes, SL 2014, 'Bacterial populations associated with early-stage adipocere formation in lacustrine waters', INTERNATIONAL JOURNAL OF LEGAL MEDICINE, vol. 128, no. 2, pp. 379-387.
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The preservation of soft tissue is a valuable evidence for forensic investigation as it may provide information about the cause and manner of death as well as the time since death. Adipocere forms from the conversion of triglycerides in the neutral fats into stable fatty acids producing a solid white product which aids tissue preservation. Adipocere will typically form in water-logged grave sites and aquatic environments. Documentation on the chemical and microbiological changes that cause adipocere formation in aquatic environments is scant and mostly based on observational case reports. The aim of this study was to monitor the early adipocere formation in lacustrine waters to investigate the effect of aquatic bacteria on adipocere formation. Tissue samples from pork (Sus scrofa domesticus) belly were submerged in water samples from Lake Ontario and deionised water (control). Bacteria samples from both water and tissue were harvested. Changes in the fatty acid composition of the tissue were determined using gas chromatography-mass spectrometry. Early-stage adipocere formation was confirmed on porcine tissue submerged in lake water but was not identified on porcine tissue submerged in deionised water. Adipocere formation required an abundance of gram-positive bacteria during the early postmortem period to assist in lipolysing the triglycerides into free fatty acids. Formation of adipocere in the lake water resulted in a decrease in bacterial concentrations in the tissue over time.

Ung, AT, Williams, SG, Angeloski, A, Ashmore, J, Kuzhiumparambil, U, Bhadbhade, M & Bishop, R 2014, 'Formation of 3-azabicyclo[3.3.1]non-3-enes: imino amides vs. imino alkenes', MONATSHEFTE FUR CHEMIE, vol. 145, no. 6, pp. 983-992.
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An effective method for synthesising alkaloidlike compounds containing the 3-azabicyclo[3.3.1]non-3-ene core structure was successfully carried out in a stereoselective manner via the bridged-Ritter reactions. Important optically active 6-alkyl(aryl)amido-4-alkyl( aryl)-2,2,6-trimethyl-3-azabicyclo[3.3.1]non-3-enes (imino amides) and 4-alkyl(aryl)-2,2,6-trimethyl-3-azabicyclo[3.3.1]nona-3,6-dienes (imino alkenes) were obtained in one step from (-)-b-pinene and the respective nitriles in the presence of concentrated H2SO4. The relative compositions of these products were controlled by varying the reaction conditions. Kinetic studies were conducted to enable a mechanistic understanding of the reaction pathways.

Veiga, A, Smith, PWF & Brown, JJ 2014, 'The Use of Sample Weights in Multivariate Multilevel Models with an Application to Income Data Collected by Using a Rotating Panel Survey', Journal of the Royal Statistical Society Series C: Applied Statistics, vol. 63, no. 1, pp. 65-84.
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SummaryLongitudinal data from labour force surveys permit the investigation of income dynamics at the individual level. However, the data often originate from surveys with a complex multistage sampling scheme. In addition, the hierarchical structure of the data that is imposed by the different stages of the sampling scheme often represents the natural grouping in the population. Motivated by how income dynamics differ between the formal and informal sectors of the Brazilian economy and the data structure of the Brazilian Labour Force Survey, we extend the probability-weighted iterative generalized least squares estimation method. Our method is used to fit multivariate multilevel models to the Brazilian Labour Force Survey data where the covariance structure between occasions at the individual level is modelled. We conclude that there are significant income differentials and that incorporating the weights in the parameter estimation has some effect on the estimated coefficients and standard errors.

Venables, SJ, Mehta, B, Daniel, R, Walsh, SJ, van Oorschot, RAH & McNevin, D 2014, 'Assessment of high resolution melting analysis as a potential SNP genotyping technique in forensic casework', ELECTROPHORESIS, vol. 35, no. 21-22, pp. 3036-3043.
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Verges, A, Steinberg, PD, Hay, ME, Poore, AGB, Campbell, AH, Ballesteros, E, Jr, HKL, Booth, DJ, Coleman, MA, Feary, DA, Figueira, W, Langlois, T, Marzinelli, EM, Mizerek, T, Mumby, PJ, Nakamura, Y, Roughan, M, van Sebille, E, Sen Gupta, A, Smale, DA, Tomas, F, Wernberg, T & Wilson, SK 2014, 'The tropicalization of temperate marine ecosystems: climate-mediated changes in herbivory and community phase shifts', PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, vol. 281, no. 1789.
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Climate-driven changes in biotic interactions can profoundly alter ecological communities, particularly when they impact foundation species. In marine systems, changes in herbivory and the consequent loss of dominant habitat forming species can result in dramatic community phase shifts, such as from coral to macroalgal dominance when tropical fish herbivory decreases, and from algal forests to 'barrens' when temperate urchin grazing increases. Here, we propose a novel phase-shift away from macroalgal dominance caused by tropical herbivores extending their range into temperate regions. We argue that this phase shift is facilitated by poleward-flowing boundary currents that are creating ocean warming hotspots around the globe, enabling the range expansion of tropical species and increasing their grazing rates in temperate areas. Overgrazing of temperate macroalgae by tropical herbivorous fishes has already occurred in Japan and the Mediterranean. Emerging evidence suggests similar phenomena are occurring in other temperate regions, with increasing occurrence of tropical fishes on temperate reefs. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Voyer, M, Gladstone, W & Goodall, H 2014, 'Understanding marine park opposition: the relationship between social impacts, environmental knowledge and motivation to fish', AQUATIC CONSERVATION-MARINE AND FRESHWATER ECOSYSTEMS, vol. 24, no. 4, pp. 441-462.
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Wagner, DM, Klunk, J, Harbeck, M, Devault, A, Waglechner, N, Sahl, JW, Enk, J, Birdsell, DN, Kuch, M, Lumibao, C, Poinar, D, Pearson, T, Fourment, M, Golding, B, Riehm, JM, Earn, DJD, DeWitte, S, Rouillard, J-M, Grupe, G, Wiechmann, I, Bliska, JB, Keim, PS, Scholz, HC, Holmes, EC & Poinar, H 2014, 'Yersinia pestis and the Plague of Justinian 541–543 AD: a genomic analysis', The Lancet Infectious Diseases, vol. 14, no. 4, pp. 319-326.
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BACKGROUND: Yersinia pestis has caused at least three human plague pandemics. The second (Black Death, 14-17th centuries) and third (19-20th centuries) have been genetically characterised, but there is only a limited understanding of the first pandemic, the Plague of Justinian (6-8th centuries). To address this gap, we sequenced and analysed draft genomes of Y pestis obtained from two individuals who died in the first pandemic. METHODS: Teeth were removed from two individuals (known as A120 and A76) from the early medieval Aschheim-Bajuwarenring cemetery (Aschheim, Bavaria, Germany). We isolated DNA from the teeth using a modified phenol-chloroform method. We screened DNA extracts for the presence of the Y pestis-specific pla gene on the pPCP1 plasmid using primers and standards from an established assay, enriched the DNA, and then sequenced it. We reconstructed draft genomes of the infectious Y pestis strains, compared them with a database of genomes from 131 Y pestis strains from the second and third pandemics, and constructed a maximum likelihood phylogenetic tree. FINDINGS: Radiocarbon dating of both individuals (A120 to 533 AD [plus or minus 98 years]; A76 to 504 AD [plus or minus 61 years]) places them in the timeframe of the first pandemic. Our phylogeny contains a novel branch (100% bootstrap at all relevant nodes) leading to the two Justinian samples. This branch has no known contemporary representatives, and thus is either extinct or unsampled in wild rodent reservoirs. The Justinian branch is interleaved between two extant groups, 0.ANT1 and 0.ANT2, and is distant from strains associated with the second and third pandemics. INTERPRETATION: We conclude that the Y pestis lineages that caused the Plague of Justinian and the Black Death 800 years later were independent emergences from rodents into human beings. These results show that rodent species worldwide represent important reservoirs for the repeated emergence of diverse lineages of Y pestis into hum...

Wand, MP 2014, 'Fully simplified multivariate normal updates in non-conjugate variational message passing', Journal of Machine Learning Research, vol. 15, pp. 1351-1369.
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Fully simplified expressions for Multivariate Normal updates in non-conjugate variational message passing approximate inference schemes are obtained. The simplicity of these expressions means that the updates can be achieved very eficiently. Since the Multivariate Normal family is the most common for approximating the joint posterior density function of a continuous parameter vector, these fully simplified updates are of great practical benefit. © 2014 Matt P. Wand.

Wang, B, Wen, Y, Ye, D, Yu, H, Sun, B, Wang, G, Hulicova-Jurcakova, D & Wang, L 2014, 'Dual Protection of Sulfur by Carbon Nanospheres and Graphene Sheets for Lithium- Sulfur Batteries', CHEMISTRY-A EUROPEAN JOURNAL, vol. 20, no. 18, pp. 5224-5230.
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Well-confined elemental sulfur was implanted into a stacked block of carbon nanospheres and graphene sheets through a simple solution process to create a new type of composite cathode material for lithium-sulfur batteries. Transmission electron microscopy and elemental mapping analysis confirm that the as-prepared composite material consists of graphene-wrapped carbon nanospheres with sulfur uniformly distributed in between, where the carbon nanospheres act as the sulfur carriers. With this structural design, the graphene contributes to direct coverage of sulfur to inhibit the mobility of polysulfides, whereas the carbon nanospheres undertake the role of carrying the sulfur into the carbon network. This composite achieves a high loading of sulfur (64.2 wt %) and gives a stable electrochemical performance with a maximum discharge capacity of 1394 mAh g-1 at a current rate of 0.1 C as well as excellent rate capability at 1 C and 2 C. The improved electrochemical properties of this composite material are attributed to the dual functions of the carbon components, which effectively restrain the sulfur inside the carbon nano-network for use in lithium-sulfur rechargeable batteries. Sulfur sandwich: A new type of sandwiched carbon network, consisting of graphene-wrapped carbon nanospheres coated with sulfur (82.7 wt % sulfur) were designed as a cathode material for lithium-sulfur rechargeable batteries (see scheme, CS=carbon sphere, GO=graphene oxide). The composite material exhibits a high specific discharge capacity of 1394 mAh g-1 at 0.1 C, excellent cycling stability for 100 cycles, and high rate performance at 1 C and 2 C. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Wangpraseurt, D, Larkum, AWD, Franklin, J, Szabo, M, Ralph, PJ & Kuhl, M 2014, 'Lateral light transfer ensures efficient resource distribution in symbiont-bearing corals', JOURNAL OF EXPERIMENTAL BIOLOGY, vol. 217, no. 4, pp. 489-498.
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Coral tissue optics has received very little attention in the past, although the interaction between tissue and light is central to our basic understanding of coral physiology. Here we used fibre-optic and electrochemical microsensors along with variable chlorophyll fluorescence imaging to directly measure lateral light propagation within living coral tissues. Our results show that corals can transfer light laterally within their tissues to a distance of ∼2cm. Such light transport stimulates O2 evolution and photosystem II operating efficiency in areas >0.5-1 cm away from direct illumination. Light is scattered strongly in both coral tissue and skeleton, leading to photon trapping and lateral redistribution within the tissue. Lateral light transfer in coral tissue is a new mechanism by which light is redistributed over the coral colony and we argue that tissue optical properties are one of the key factors in explaining the high photosynthetic efficiency of corals. © 2014. Published by The Company of Biologists Ltd.

Wangpraseurt, D, Polerecky, L, Larkum, AWD, Ralph, PJ, Nielsen, DA, Pernice, M & Kuhl, M 2014, 'The in situ light microenvironment of corals', LIMNOLOGY AND OCEANOGRAPHY, vol. 59, no. 3, pp. 917-926.
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We used a novel diver-operated microsensor system to collect in situ spectrally resolved light fields on corals with a micrometer spatial resolution. The light microenvironment differed between polyp and coenosarc tissues with scalar irradiance (400700 nm) over polyp tissue, attenuating between 5.1- and 7.8-fold from top to base of small hemispherical coral colonies, whereas attenuation was at most 1.5-fold for coenosarc tissue. Fluctuations in ambient solar irradiance induced changes in light and oxygen microenvironments, which were more pronounced and faster in coenosarc compared with polyp tissue. Backscattered light from the surrounding benthos contributed . 20% of total scalar irradiance at the coral tissue surface and enhanced symbiont photosynthesis and the local O2 concentration, indicating an important role of benthos optics for coral ecophysiology. Light fields on corals are species and tissue specific and exhibit pronounced variation on scales from micrometers to decimeters. Consequently, the distribution, genetic diversity, and physiology of coral symbionts must be coupled with the measurements of their actual light microenvironment to achieve a more comprehensive understanding of coral ecophysiology.

Wangpraseurt, D, Tamburic, B, Szabo, M, Suggett, D, Ralph, PJ & Kuhl, M 2014, 'Spectral Effects on Symbiodinium Photobiology Studied with a Programmable Light Engine', PLOS ONE, vol. 9, no. 11.
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©2014 Wangpraseurt et al. The spectral light field of Symbiodinium within the tissue of the coral animal host can deviate strongly from the ambient light field on a coral reef and that of artificial light sources used in lab studies on coral photobiology. Here, we used a novel approach involving light microsensor measurements and a programmable light engine to reconstruct the spectral light field that Symbiodinium is exposed to inside the coral host and the light field of a conventional halogen lamp in a comparative study of Symbiodinium photobiology. We found that extracellular gross photosynthetic O 2 evolution was unchanged under different spectral illumination, while the more red-weighted halogen lamp spectrum decreased PSII electron transport rates and there was a trend towards increased light-enhanced dark respiration rates under excess irradiance. The approach provided here allows for reconstructing and comparing intra-tissue coral light fields and other complex spectral compositions of incident irradiance. This novel combination of sensor technologies provides a framework to studying the influence of macro- and microscale optics on Symbiodinium photobiology with unprecedented spectral resolution.

Watanabe, K, Miyoshi, Y, Kubo, F, Onuma, R, Murray, S & Horiguchi, T 2014, 'Ankistrodinium armigerum sp. nov. (Dinophyceae), a new species of heterotrophic marine sand-dwelling dinoflagellate from Japan and Australia', PHYCOLOGICAL RESEARCH, vol. 62, no. 2, pp. 125-135.
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A new heterotrophic sand-dwelling dinoflagellate, Ankistrodinium armigerum K. Watanabe, Miyoshi, Kubo, Murray et Horiguchi sp. nov., is described from Ishikari Beach, Hokkaido, Japan and Port Botany, NSW, Australia. The dinoflagellate is laterally compressed, possessing a short triangular epicone and a large sac-like hypocone. It possesses a right-handed cingulum and a deeply-incised sulcus. The sulcus descends towards the posterior of the cell where it becomes much deeper and wider, resulting in a bilobed ventral side to the hypocone, with a greater excavation of the left lobe than the right. In addition, the right lobe of the hypocone is shorter than the left lobe, which allows a partial view of the left sulcal wall when the cell is viewed from its right side. The sulcus ascends in the epicone to form an apical groove. The apical groove is linear but terminates in an ellipsoid fashion and its extremity approaches, but does not form a closed loop with the apical end of the linear portion. The dinoflagellate possesses two distinct size classes of trichocysts. The large trichocysts are located in the posterior part of the cell, while small trichocysts are distributed throughout the cell. The dinoflagellate shares morphological characteristics with the heterotrophic sand-dwelling dinoflagellate, Ankistrodinium semilunatum, the type species of the genus. These include a laterally compressed cell, a right-handed cingulum, a deeply-incised sulcus and the same basic structure to the apical groove. Molecular phylogenetic analyses based on small and large subunits of rDNA showed that in both trees, A. semilunatum and A. armigerum formed a robust clade, suggesting that these two species are closely related. Because no organism with the characteristics of this species exists and because this species is closely related to A. semilunatum, we concluded that this species should be described as a second species of the genus Ankistrodinium.

Webb, JK, Letnic, M, Jessop, TS & Dempster, T 2014, 'Behavioural flexibility allows an invasive vertebrate to survive in a semi-arid environment', BIOLOGY LETTERS, vol. 10, no. 2.
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Plasticity or evolution in behavioural responses are key attributes of successful animal invasions. In northern Australia, the invasive cane toad (Rhinella marina) recently invaded semi-arid regions. Here, cane toads endure repeated daily bouts of severe desiccation and thermal stress during the long dry season (April-October).We investigated whether cane toads have shifted their ancestral nocturnal rehydration behaviour to one that exploits water resources during the day. Such a shift in hydration behaviour could increase the fitness of individual toads by reducing exposure to desiccation and thermal stress suffered during the day even within terrestrial shelters.We used a novel method (acoustic tags) to monitor the daily hydration behaviour of 20 toads at two artificial reservoirs on Camfield station, Northern Territory. Remarkably, cane toads visited reservoirs to rehydrate during daylight hours, with peaks in activity between 9.00 and 17.00. This diurnal pattern of rehydration activity contrasts with nocturnal rehydration behaviour exhibited by adult toads in their native geographical range and more mesic parts of Australia. Our results demonstrate that cane toads phase shift a key behaviour to survive in a harsh semi-arid landscape. Behavioural phase shifts have rarely been reported in invasive species but could facilitate ongoing invasion success. © 2014 The Author(s) Published by the Royal Society.

Wei, Y, Chen, S, Su, D, Sun, B, Zhu, J & Wang, G 2014, '3D mesoporous hybrid NiCo2O4@graphene nanoarchitectures as electrode materials for supercapacitors with enhanced performances', JOURNAL OF MATERIALS CHEMISTRY A, vol. 2, no. 21, pp. 8103-8109.
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3D mesoporous hybrid NiCo2O4@graphene nanoarchitectures were successfully synthesized by a combination of freeze drying and hydrothermal reaction. Field-emission scanning electron microscopy (FESEM) and TEM analyses revealed that the NiCo2O 4@graphene nanostructures consist of a hierarchical mesoporous sheet-on-sheet nanoarchitecture with a high specific surface area of 194 m 2 g-1. Ultrathin NiCo2O4 nanosheets, with a thickness of a few nanometers and mesopores ranging from 2 to 5 nm, were wrapped in graphene nanosheets and hybrid nanoarchitectures were formed. When applied as electrode materials in supercapacitors, the hybrid NiCo 2O4@graphene nanosheets exhibited a high capacitance of 778 F g-1 at a current density of 1 A g-1, and an excellent cycling performance extending to 10000 cycles at a high current density of 10 A g-1. This journal is © the Partner Organisations 2014.

Welsh, P, Woodward, M, Hillis, GS, Li, Q, Marre, M, Williams, B, Poulter, N, Ryan, L, Harrap, S, Patel, A, Chalmers, J & Sattar, N 2014, 'Do Cardiac Biomarkers NT-proBNP and hsTnT Predict Microvascular Events in Patients With Type 2 Diabetes? Results From the ADVANCE Trial', DIABETES CARE, vol. 37, no. 8, pp. 2202-2210.
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Wen, B, Combes, V, Bonhoure, A, Weksler, BB, Couraud, P-O & Grau, GER 2014, 'Endotoxin-Induced Monocytic Microparticles Have Contrasting Effects on Endothelial Inflammatory Responses', PLoS ONE, vol. 9, no. 3, pp. e91597-e91597.
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Septic shock is a severe disease state characterised by the body's life threatening response to infection. Complex interactions between endothelial cells and circulating monocytes are responsible for microvasculature dysfunction contributing to the pathogenesis of this syndrome. Here, we intended to determine whether microparticles derived from activated monocytes contribute towards inflammatory processes and notably vascular permeability. We found that endotoxin stimulation of human monocytes enhances the release of microparticles of varying phenotypes and mRNA contents. Elevated numbers of LPS-induced monocytic microparticles (mMP) expressed CD54 and contained higher levels of transcripts for pro-inflammatory cytokines such as TNF, IL-6 and IL-8. Using a prothrombin time assay, a greater reduction in plasma coagulation time was observed with LPS-induced mMP than with non-stimulated mMP. Co-incubation of mMP with the human brain endothelial cell line hCMEC/D3 triggered their time-dependent uptake and significantly enhanced endothelial microparticle release. Unexpectedly, mMP also modified signalling pathways by diminishing pSrc (tyr416) expression and promoted endothelial monolayer tightness, as demonstrated by endothelial impedance and permeability assays. Altogether, these data strongly suggest that LPS-induced mMP have contrasting effects on the intercellular communication network and display a dual potential: enhanced pro-inflammatory and procoagulant properties, together with protective function of the endothelium. © 2014 Wen et al.

Wen, S, Zhao, Q, An, X, Zhu, J, Hou, W, Li, K, Huang, Y, Shen, M, Zhu, W & Shi, X 2014, 'Multifunctional PEGylated Multiwalled Carbon Nanotubes for Enhanced Blood Pool and Tumor MR Imaging', Advanced Healthcare Materials, vol. 3, no. 10, pp. 1568-1577.
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West, J & Platen, E 2014, 'Natural Disasters, Insurance Stocks and the Numeraire Portfolio', Advances in Quantitative Analysis of Finance and Accounting, vol. 12, pp. 23-58.
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This study employs a generalized numeraire portfolio to benchmark insurance stocks to detect abnormal returns in the presence of natural disasters and insurable losses. We show that under the benchmark approach the efficient markets hypothesis holds in the presence of extreme insurable loss whereas other common methods such as the market model and Fama- French three factor model often fail due to the accumulation of estimation errors. We construct a portfolio of U.S. insurance firms and observe the market reaction to a set of major insured natural disasters. Numeraire denominated or benchmarked returns are shown to be are natural measures of abnormal returns. Using the benchmark approach we observe no significant trend in the cumulative abnormal returns of insurance securities following a natural disaster. Using both the traditional market model and the Fama-French three factor model however, we observe significantly positive cumulative abnormal returns following an insured event. The errors inherent in the market model and three-factor model for event studies are shown to be eliminated using the benchmark approach.

Wheway, J, Latham, SL, Combes, V & Grau, GER 2014, 'Endothelial Microparticles Interact with and Support the Proliferation of T Cells', The Journal of Immunology, vol. 193, no. 7, pp. 3378-3387.
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Abstract Endothelial cells closely interact with circulating lymphocytes. Aggression or activation of the endothelium leads to an increased shedding of endothelial cell microparticles (MP). Endothelial MP (EMP) are found in high plasma levels in numerous immunoinflammatory diseases, such as atherosclerosis, sepsis, multiple sclerosis, and cerebral malaria, supporting their role as effectors and markers of vascular dysfunction. Given our recently described role for human brain microvascular endothelial cells (HBEC) in modulating immune responses, we investigated how HBEC-derived MP could interact with and support the proliferation of T cells. Like their mother cells, EMP expressed molecules important for Ag presentation and T cell costimulation, that is, β2-microglobulin, MHC II, CD40, and ICOSL. HBEC were able to take up fluorescently labeled Ags with EMP also containing fluorescent Ags, suggestive of Ag carryover from HBEC to EMP. In cocultures, fluorescently labeled EMP from resting or cytokine-stimulated HBEC formed conjugates with both CD4+ and CD8+ subsets, with higher proportions of T cells binding EMP from cytokine-stimulated cells. The increased binding of EMP from cytokinestimulated HBEC to T cells was VCAM-1 and ICAM-1 dependent. Finally, in CFSE T cell proliferation assays using anti-CD3 mAb or T cell mitogens, EMP promoted the proliferation of CD4+ T cells and that of CD8+ T cells in the absence of exogenous stimuli and in the T cell mitogenic stimulation. Our findings provide novel evidence that EMP can enhance T cell activation and potentially ensuing Ag presentation, thereby pointing toward a novel role for MP in neuroimmunological complications of infectious diseases.

Wiese, M, Murray, SA, Alvin, A & Neilan, BA 2014, 'Gene expression and molecular evolution of sxtA4 in a saxitoxin producing dinoflagellate Alexandrium catenella', TOXICON, vol. 92, pp. 102-112.
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Williams, DBG, George, MJ & Marjanovic, L 2014, 'Rapid Detection of Atrazine and Metolachlor in Farm Soils: Gas Chromatography–Mass Spectrometry-Based Analysis Using the Bubble-in-Drop Single Drop Microextraction Enrichment Method', Journal of Agricultural and Food Chemistry, vol. 62, no. 31, pp. 7676-7681.
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Tracking of metolachlor and atrazine herbicides in agricultural soils, from spraying through to harvest, was conducted using our recently reported 'bubble-in-drop single-drop microextraction' method. The method showed good linearity (R2 = 0.999 and 0.999) in the concentration range of 0.01-1.0 ng/mL with LOD values of 0.01 and 0.02 ng/mL for atrazine and metolachlor, respectively. Sonication methods were poor at releasing these herbicides from the soil matrixes, while hot water extraction readily liberated them, providing an efficient accessible alternative to sonication techniques. Good recoveries of 97% and 105% were shown for atrazine and metolachlor, respectively, from the soil. The spiking protocol was also investigated, resulting in a traceless spiking method. We demonstrate a very sensitive technique by which to assess, for example, the length of residence of pesticides in given soils and thus risk of exposure. © 2014 American Chemical Society.

Wolff, C, Soref, R, Poulton, CG & Eggleton, BJ 2014, 'Germanium as a material for stimulated Brillouin scattering in the mid-infrared', Optics Express, vol. 22, no. 25, pp. 30735-30735.
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© 2014 Optical Society of America. In a theoretical design study, we propose buried waveguides made of germanium or alloys of germanium and other group-IV elements as a CMOS-compatible platform for robust, high-gain stimulated Brillouin scattering (SBS) applications in the mid-infrared regime. To this end, we present numerical calculations for backward-SBS at 4mm in germanium waveguides that are buried in silicon nitride. Due to the strong photoelastic anisotropy of germanium, we investigate two different orientations of the germanium crystal with respect to the waveguide's propagation direction and find considerable differences. The acoustic wave equation is solved including crystal anisotropy; acoustic losses are computed from the acoustic mode patterns and previously published material parameters.

Wolff, C, Steel, MJ & Poulton, CG 2014, 'Formal selection rules for Brillouin scattering in integrated waveguides and structured fibers', Optics Express, vol. 22, no. 26, pp. 32489-32501.
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We derive formal selection rules for Stimulated Brillouin Scattering (SBS) instructured waveguides. Using a group-theoretical approach, we show how thewaveguide symmetry determines which optical and acoustic modes interact forboth forward and backward SBS. We present a general framework for determiningthis interaction and give important examples for SBS in waveguides withrectangular, triangular and hexagonal symmetry. The important role played bydegeneracy of the optical modes is illustrated. These selection rules areimportant for SBS-based device design and for a full understanding the physicsof SBS in structured waveguides.

Wolff, C, Steel, MJ, Eggleton, BJ & Poulton, CG 2014, 'Stimulated Brillouin Scattering in integrated photonic waveguides: forces, scattering mechanisms and coupled mode analysis', Phys. Rev. A, vol. 92, no. 1, p. 013836.
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Recent theoretical studies of Stimulated Brillouin Scattering (SBS) innanoscale devices have led to an intense research effort dedicated to thedemonstration and application of this nonlinearity in on-chip systems. The keyfeature of SBS in integrated photonic waveguides is that small, high-contrastwaveguides are predicted to experience powerful optical forces on the waveguideboundaries, which are predicted to further boost the SBS gain that is alreadyexpected to grow dramatically in such structures because of the higher modeconfinement alone. In all recent treatments, the effect of radiation pressureis included separately from the scattering action that the acoustic fieldexerts on the optical field. In contrast to this, we show here that the effectsof radiation pressure and motion of the waveguide boundaries are inextricablylinked. Central to this insight is a new formulation of the SBS interactionthat unifies the treatment of light and sound, incorporating all relevantinteraction mechanisms --- radiation pressure, waveguide boundary motion,electrostriction and photoelasticity --- from a rigorous thermodynamicperspective. Our approach also clarifies important points of ambiguity in theliterature, such as the nature of edge-effects with regard to electrostriction,and of body-forces with respect to radiation pressure. This new perspective onBrillouin processes leads to physical insight with implications for the designand fabrication of SBS-based nanoscale devices.

Wood, LK & Langford, SJ 2014, 'Motor Neuron Disease: A Chemical Perspective', Journal of Medicinal Chemistry, vol. 57, no. 15, pp. 6316-6331.
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Wood, RJ, Mitrovic, SM & Kefford, BJ 2014, 'Determining the relative sensitivity of benthic diatoms to atrazine using rapid toxicity testing: A novel method', SCIENCE OF THE TOTAL ENVIRONMENT, vol. 485, pp. 421-427.
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Herbicides pose a potential threat to aquatic ecosystems, especially to phototrophic organisms such as benthic diatoms. Benthic diatoms may be a valuable indicator of the toxic impacts of herbicides in aquatic systems. However, this requires information on the herbicide sensitivity of a wide range of freshwater benthic diatom taxa. Unfortunately this information is only available for a limited number of species as current methods of developing new algae toxicity tests on individual taxa are lengthy and costly. To address this issue, we developed a new rapid toxicity test method to test natural benthic communities, from which the relative herbicide sensitivity of many individual taxa can be derived. This involved the collection of natural benthic communities from rocks in situ, which were placed directly into laboratory toxicity tests. Sensitivity data for several diatom genera in a 48 hour exposure toxicity test were produced, without the need for cultures or multiple site visits. After exposure to the highest treatment of atrazine (500 µg L- 1) there were significant declines of healthy cells in the most sensitive genera: Gomphonema declined by 74%, Amphora by 62%, Cymbella by 54% and Ulnaria by 34% compared to control levels. In contrast, the genera, Eunotia, Achnanthidium and Navicula, had no statistically significant decline in cell health. This method can identify the diatom taxa most at risk of herbicide toxicity within the natural benthic diatom community. The rapid toxicity testing method presented is a simple and effective method to obtain sensitivity data for multiple taxa within a natural benthic diatom community in a relatively short period of time.

Woolf, A, Puchtler, T, Aharonovich, I, Zhu, T, Niu, N, Wang, D, Oliver, R & Hu, EL 2014, 'Distinctive signature of indium gallium nitride quantum dot lasing in microdisk cavities', PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 111, no. 39, pp. 14042-14046.
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Low-threshold lasers realized within compact, high-quality optical cavities enable a variety of nanophotonics applications. Gallium nitride materials containing indium gallium nitride (InGaN) quantum dots and quantum wells offer an outstanding platform to study light-matter interactions and realize practical devices such as efficient light-emitting diodes and nanolasers. Despite progress in the growth and characterization of InGaN quantum dots, their advantages as the gain medium in low-threshold lasers have not been clearly demonstrated. This work seeks to better understand the reasons for these limitations by focusing on the simpler, limitedmode microdisk cavities, and by carrying out comparisons of lasing dynamics in those cavities using varying gain media including InGaN quantum wells, fragmented quantum wells, and a combination of fragmented quantum wells with quantum dots. For each gain medium, we use the distinctive, high-quality (Q∼5,500) modes of the cavities, and the change in the highest-intensity mode as a function of pump power to better understand the dominant radiative processes. The variations of threshold power and lasing wavelength as a function of gain medium help us identify the possible limitations to lower-threshold lasing with quantum dot active medium. In addition, we have identified a distinctive lasing signature for quantum dot materials, which consistently lase at wavelengths shorter than the peak of the room temperature gain emission. These findings not only provide better understanding of lasing in nitride-based quantum dot cavity systems but also shed insight into the more fundamental issues of light-matter coupling in such systems.

Woolley, LK, Fell, SA, Gonsalves, JR, Raymond, BBA, Collins, D, Kuit, TA, Walker, MJ, Djordjevic, SP, Eamens, GJ & Jenkins, C 2014, 'Evaluation of recombinant Mycoplasma hyopneumoniae P97/P102 paralogs formulated with selected adjuvants as vaccines against mycoplasmal pneumonia in pigs', Vaccine, vol. 32, no. 34, pp. 4333-4341.
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Pig responses to recombinant subunit vaccines containing fragments of eight multifunctional adhesins of the Mycoplasma hyopneumoniae (Mhp) P97/P102 paralog family formulated with Alhydrogel(®) or Montanide™ Gel01 were compared with a commercial bacterin following experimental challenge. Pigs, vaccinated intramuscularly at 9, 12 and 15 weeks of age with either of the recombinant formulations (n=10 per group) or Suvaxyn(®) M. hyo (n=12), were challenged with Mhp strain Hillcrest at 17 weeks of age. Unvaccinated, challenged pigs (n=12) served as a control group. Coughing was assessed daily. Antigen-specific antibody responses were monitored by ELISA in serum and tracheobronchial lavage fluid (TBLF), while TBLF was also assayed for cytokine responses (ELISA) and bacterial load (qPCR). At slaughter, gross and histopathology of lungs were quantified and damage to epithelial cilia in the porcine trachea was evaluated by scanning electron microscopy. Suvaxyn(®) M. hyo administration induced significant serological responses against Mhp strain 232 whole cell lysates (wcl) and recombinant antigen F3P216, but not against the remaining vaccine subunit antigens. Alhydrogel(®) and Montanide™ Gel01-adjuvanted antigen induced significant antigen-specific IgG responses, with the latter adjuvant eliciting comparable Mhp strain 232 wcl specific IgG responses to Suvaxyn(®) M. hyo. No significant post-vaccination antigen-specific mucosal responses were detected with the recombinant vaccinates. Suvaxyn(®) M. hyo was superior in reducing clinical signs, lung lesion severity and bacterial load but the recombinant formulations offered comparable protection against cilial damage. Lower IL-1β, TNF-α and IL-6 responses after challenge were associated with reduced lung lesion severity in Suvaxyn(®) M. hyo vaccinates, while elevated pathology scores in recombinant vaccinates corresponded to cytokine levels that were similarly elevated as in unvaccinated pigs. This study highlights the need fo...

Wright, EP, Prasad, KAG, Padula, MP & Coorssen, JR 2014, 'Deep Imaging: How Much of the Proteome Does Current Top-Down Technology Already Resolve?', PLoS ONE, vol. 9, no. 1, pp. e86058-e86058.
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Effective proteome analyses are based on interplay between resolution and detection. It had been claimed that resolution was the main factor limiting the use of two-dimensional gel electrophoresis. Improved protein detection now indicates that this is unlikely to be the case. Using a highly refined protocol, the rat brain proteome was extracted, resolved, and detected. In order to overcome the stain saturation threshold, high abundance protein species were excised from the gel following standard imaging. Gels were then imaged again using longer exposure times, enabling detection of lower abundance, less intensely stained protein species. This resulted in a significant enhancement in the detection of resolved proteins, and a slightly modified digestion protocol enabled effective identification by standard mass spectrometric methods. The data indicate that the resolution required for comprehensive proteome analyses is already available, can assess multiple samples in parallel, and preserve critical information concerning post-translational modifications. Further optimization of staining and detection methods promises additional improvements to this economical, widely accessible and effective top-down approach to proteome analysis. © 2014 Wright et al.

Wu, CW, Solntsev, AS, Neshev, DN & Sukhorukov, AA 2014, 'Photon pair generation and pump filtering in nonlinear adiabatic waveguiding structures', Optics Letters, vol. 39, no. 4, pp. 953-956.
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We propose a novel integrated scheme for generation of Bell states, which allows simultaneous spatial filtering of pump photons. It is achieved through spontaneous parametric down-conversion in the system of nonlinear adiabatically coupled waveguides. We perform detailed analytic study of photon-pair generation in coupled waveguides and reveal the optimal conditions for the generation of each particular Bell state. Furthermore, we simulate the performance of the device under realistic assumptions and show that adiabatic coupling allows us to spatially filter the pump from modal-entangled photon pairs. Finally, we demonstrate that adiabatic couplers open the possibility of maintaining the purity of generated Bell states in a relatively fabrication-fault-tolerant way. © 2014 Optical Society of America.

Wu, H, Yang, Z, Liao, J, Lai, S, Qiu, J, Song, Z, Yang, Y & Zhou, D 2014, 'Enhancement of near-infrared to near-infrared upconversion emission in the CeO_2: Er^3+, Tm^3+, Yb^3+ inverse opals', Optics Letters, vol. 39, no. 4, pp. 918-918.
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Wu, H, Yang, Z, Liao, J, Lai, S, Qiu, J, Song, Z, Yang, Y, Zhou, D & Yin, Z 2014, 'Upconversion luminescence properties of three-dimensional ordered macroporous CeO2: Er3+, Yb3+', Journal of Alloys and Compounds, vol. 586, pp. 485-487.
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Wu, Y, Campbell, DA, Irwin, AJ, Suggett, DJ & Finkel, ZV 2014, 'Ocean acidification enhances the growth rate of larger diatoms', Limnology and Oceanography, vol. 59, no. 3, pp. 1027-1034.
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Ocean acidification is changing the nature of inorganic carbon availability in the global oceans. Diatoms account for µ 40% of all marine primary productivity and are major contributors to the export of atmospheric carbon to the deep ocean. Larger diatoms are more likely to be stimulated by future increases in CO2 availability as a result of their low surface area to volume ratio and lower diffusive flux of CO2 relative to their carbon demand for growth. Here we quantify the effect of the partial pressure of carbon dioxide (PCO2), at levels of 190, 380, and 750 µL L−1, on the growth rate, photosystem II electron transport rate (ETR), and elemental composition for five diatom species ranging over five orders of magnitude in cell volume. Growth rates for all species were enhanced under 750 relative to 190 and 380 µL L−1, with little change in ETR or elemental stoichiometries, indicating an enhanced allocation of photochemical energy to growth under elevated PCO2. PCO2 enhancement of growth rates was size dependent. Under 750 vs. 190 µL L−1 partial pressures, growth rate was enhanced by µ 5% for the smaller diatom species to µ 30% for the largest species examined. The size dependence of CO2‐stimulated growth enhancement indicates that ocean acidification may selectively favor an increase in the growth rates of larger vs. smaller phytoplankton species in the sea, with potentially significant consequences for carbon biochemistry.

Wu, Y, El Ali, BM, Hussein, I, Guan, S, Wang, GX, Zhou, A & Zhang, M 2014, 'Special Issue: Novel Materials and Their Synthesis', Arabian Journal for Science and Engineering, vol. 39, no. 9, pp. 6587-6587.
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Wu, Y, Guo, R, Wen, S, Shen, M, Zhu, M, Wang, J & Shi, X 2014, 'Folic acid-modified laponite nanodisks for targeted anticancer drug delivery', J. Mater. Chem. B, vol. 2, no. 42, pp. 7410-7418.
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Folic acid-modified laponite nanodisks can be used as an efficient platform for targeted delivery of doxorubicinviaa receptor-mediated pathway.

Wu, Y, Jeans, J, Suggett, DJ, Finkel, ZV & Campbell, DA 2014, 'Large centric diatoms allocate more cellular nitrogen to photosynthesis to counter slower RUBISCO turnover rates', Frontiers in Marine Science, vol. 1, no. DEC, pp. 1-11.
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© 2014 Wu, Jeans, Suggett, Finkel and Campbell. Diatoms contribute ~40% of primary production in the modern ocean and encompass the largest cell size range of any phytoplankton group. Diatom cell size influences their nutrient uptake, photosynthetic light capture, carbon export efficiency, and growth responses to increasing pCO2. We therefore examined nitrogen resource allocations to the key protein complexes mediating photosynthesis across six marine centric diatoms, spanning 5 orders of magnitude in cell volume, under past, current and predicted future pCO2 levels, in balanced growth under nitrogen repletion. Membrane bound photosynthetic protein concentrations declined with cell volume in parallel with cellular concentrations of total protein, total nitrogen and chlorophyll. Larger diatom species, however, allocated a greater fraction (by 3.5-fold) of their total cellular nitrogen to the soluble Ribulose-1,5-bisphosphate Carboxylase Oxygenase (RUBISCO) carbon fixation complex than did smaller species. Carbon assimilation per unit of RUBISCO large subunit (C RbcL-1 s-1) decreased with cell volume, from ~8 to ~2 C RbcL-1 s-1 from the smallest to the largest cells. Whilst a higher allocation of cellular nitrogen to RUBISCO in larger cells increases the burden upon their nitrogen metabolism, the higher RUBISCO allocation buffers their lower achieved RUBISCO turnover rate to enable larger diatoms to maintain carbon assimilation rates per total protein comparable to small diatoms. Individual species responded to increased pCO2, but cell size effects outweigh pCO2 responses across the diatom species size range examined. In large diatoms a higher nitrogen cost for RUBISCO exacerbates the higher nitrogen requirements associated with light absorption, so the metabolic cost to maintain photosynthesis is a cell size-dependent trait.

Wu, Y, Wang, G & Guan, S 2014, 'Novel Materials and Their Synthesis', Chemistry International, vol. 36, no. 2, pp. 26-27.
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Xie, H, Jin, D, Yu, J, Peng, T, Ding, Y, Zhou, C & Xi, P 2014, 'Schlieren confocal microscopy for phase-relief imaging', OPTICS LETTERS, vol. 39, no. 5, pp. 1238-1241.
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We demonstrate a simple phase-sensitive microscopic technique capable of imaging the phase gradient of a transparent specimen, based on the Schlieren modulation and confocal laser scanning microscopy (CLSM). The incident laser is refracted by the phase gradient of the specimen and excites a fluorescence plate behind the specimen to create a secondary illumination; then the fluoresence is modulated by a partial obstructor before entering the confocal pinhole. The quantitative relationship between the image intensity and the sample phase gradient can be derived. This setup is very easy to be adapted to current confocal setups, so that multimodality fluorescence/structure images can be obtained within a single system.

Xie, X, Su, D, Chen, S, Zhang, J, Dou, S & Wang, G 2014, 'SnS₂ Nanoplatelet@Graphene Nanocomposites as High‐Capacity Anode Materials for Sodium‐Ion Batteries', Chemistry – An Asian Journal, vol. 9, no. 6, pp. 1611-1617.
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AbstractNa‐ion batteries have been attracting intensive investigations as a possible alternative to Li‐ion batteries. Herein, we report the synthesis of SnS2 nanoplatelet@graphene nanocomposites by using a morphology‐controlled hydrothermal method. The as‐prepared SnS2/graphene nanocomposites present a unique two‐dimensional platelet‐on‐sheet nanoarchitecture, which has been identified by scanning and transmission electron microscopy. When applied as the anode material for Na‐ion batteries, the SnS2/graphene nanosheets achieved a high reversible specific sodium‐ion storage capacity of 725 mA h g−1, stable cyclability, and an enhanced high‐rate capability. The improved electrochemical performance for reversible sodium‐ion storage could be ascribed to the synergistic effects of the SnS2 nanoplatelet/graphene nanosheets as an integrated hybrid nanoarchitecture, in which the graphene nanosheets provide electronic conductivity and cushion for the active SnS2 nanoplatelets during Na‐ion insertion and extraction processes.

Xie, X, Su, D, Huang, X, Dou, SX & Wang, G 2014, 'Solvothermal Synthesis of Co₃S₄/Graphene Nanoassemblies As Anode Materials for Lithium-Ion Batteries', ECS Meeting Abstracts, vol. MA2014-04, no. 2, pp. 310-310.
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Co3S4/graphene nanoassemblies were synthesized by a facile solvothermal approach, in which bifunctional dimethyl sulfoxide served as both solvent and sulfur-source. Structural characterizations reveal an intimate contact between Co3S4 and graphene matrix. When employed as anode materials for lithium-ion batteries, the Co3S4/graphene nanoassemblies exhibited good electrochemical performance, including a high reversible capacity of 1085 mAh/g, good cyclability and excellent rate capability. Compared to bare Co3S4 and graphene, the lithium-ion storage performance has been significantly improved. The improved electrochemical performance for reversible lithium-ion storage could be ascribed to the synergistic effects of the Co3S4/graphene nanoassemblies as an integrated hybrid nanoarchitecture, in which graphene nanosheets provide electronic conductivity, serve as the homogeneous dispersive agent and offer buffer layers for the active Co3S4 during lithium-ion insertion and extraction processes.

Xie, X, Su, D, Sun, B, Zhang, J, Wang, C & Wang, G 2014, 'Synthesis of Single-Crystalline Spinel LiMn2O4 Nanorods for Lithium-Ion Batteries with High Rate Capability and Long Cycle Life', CHEMISTRY-A EUROPEAN JOURNAL, vol. 20, no. 51, pp. 17125-17131.
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© 2014 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim. The long-standing challenge associated with capacity fading of spinel LiMn2O4 cathode material for lithiumion batteries is investigated. Single-crystalline spinel LiMn2O4 nanorods were successfully synthesized by a template-engaged method. Porous Mn3O4 nanorods were used as selfsacrificial templates, into which LiOH was infiltrated by a vacuum-assisted impregnation route. When used as cathode materials for lithium-ion batteries, the spinel LiMn2O4 nanorods exhibited superior long cycle life owing to the one-dimensional nanorod structure, single-crystallinity, and Li-rich effect. LiMn2O4 nanorods retained 95.6% of the initial capacity after 1000 cycles at 3C rate. In particular, the nanorod morphology of the spinel LiMn2O4 was well-preserved after a long-term cycling, suggesting the ultrahigh structural stability of the single crystalline spinel LiMn2O4 nanorods. This result shows the promising applications of single-crystalline spinel LiMn2O4 nanorods as cathode materials for lithium-ion batteries with high rate capability and long cycle life.

Xuefeng, X, Jian’ang, L, Xu, H, Chenye, S, Dayong, J & Wenhui, L 2014, 'Clinical characteristics and prognostic factors of patients with gastric neuroendocrine carcinoma treated with radical surgery', Chinese Medical Journal, vol. 127, no. 13, pp. 2419-2422.
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Background Gastric neuroendocrine carcinomas (g-NECs) are rare tumors that have aggressive biological behaviors and poor prognosis, but the prognostic factors of postoperative patients with g-NEC are still unclear. Our aim was to study and explore the clinical characteristics and prognostic factors of patients with g-NEC treated with radical surgery. Methods The clinical data of 43 g-NEC patients who underwent surgery from January 2002 to January 2011 at the Zhongshan Hospital of Fudan University were analyzed. Follow-up was conducted by telephone, mail, or returning visit survey. Results The sizes of the 43 neuroendocrine carcinomas (G3) were 1.5 cm × 1.5 cm × 0.5 cm to 7 cm × 8 cm × 1.5 cm. Eight NECs were localized, and 35 had lymph node involvement, of which 1 also had hepatic metastasis. At the end of the follow-up, the follow-up rate was 97.7% (42/43), and the median follow-up time was 22.2 months. The median overall survival of g-NEC patients was 36.5 months, and the 1-, 3-, and 5-year overall survival rates were 86.0%, 51.6%, and 36.7%, respectively. Sex (P <0.05) and lymph node involvement (P <0.05) were prognostic factors of postoperative g-NEC patients, among which sex was an independent prognostic factor (P <0.05), as a survival advantage of female patients over male was observed. Conclusions Most of the g-NECs were diagnosed at an advanced stage. The prognosis of g-NECs was related with sex and lymph node involvement, of which...

Yagoub, D, Wilkins, MR, Lay, AJ, Kaczorowski, DC, Hatoum, D, Bajan, S, Hutvagner, G, Lai, JH, Wu, W, Martiniello-Wilks, R, Xia, P & McGowan, EM 2014, 'Sphingosine Kinase 1 Isoform-Specific Interactions in Breast Cancer', MOLECULAR ENDOCRINOLOGY, vol. 28, no. 11, pp. 1899-1915.
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© 2014 by the Endocrine Society. Sphingosine kinase 1 (SK1) is a signaling enzyme that catalyzes the formation of sphingosine-1-phosphate. Overexpression of SK1 is causally associated with breast cancer progression and resistance to therapy. SK1 inhibitors are currently being investigated as promising breast cancer therapies. Two major transcriptional isoforms, SK143kDa and SK151kDa, have been identified; however, the 51kDa variant is predominant in breast cancer cells. No studies have investigated the protein-protein interactions of the 51kDa isoform and whether the two SK1 isoforms differ significantly in their interactions. Seeking an understanding of the regulation and role of SK1, we used a triple-labeling stable isotope labeling by amino acids in cell culture-based approach to identify SK1-interacting proteins common and unique to both isoforms. Of approximately 850 quantified proteins in SK1 immunopre-cipitates, a high-confidence list of 30 protein interactions with each SK1 isoform was generated via a meta-analysis of multiple experimental replicates. Many of the novel identified SK1 interaction partners such assupervillin, drebrin, and the myristoylated alanine-rich C-kinase substrate-related protein supported and highlighted previously implicated roles of SK1 in breast cancer cell migration, adhesion, and cytoskeletal remodeling. Of these interactions, several were found to be exclusive to the 43kDa isoform of SK1, including the protein phosphatase 2A, a previously identified SK1-interacting protein. Other proteins such as allograft inflammatory factor 1-like protein, the latent-transforming growth factor β-binding protein, and dipeptidyl peptidase 2 were found to associate exclusively with the 51kDa isoform of SK1. In this report, we have identified common and isoform-specificSK1-interacting partners that provide insight into the molecular mechanisms that drive SK1-mediated oncogenicity.

Yan, J, Ouyang, R, Jensen, PS, Ascic, E, Tanner, D, Mao, B, Zhang, J, Tang, C, Hush, NS, Ulstrup, J & Reimers, JR 2014, 'Controlling the Stereochemistry and Regularity of Butanethiol Self-Assembled Monolayers on Au(111)', Journal of the American Chemical Society, vol. 136, no. 49, pp. 17087-17094.
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© 2014 American Chemical Society. The rich stereochemistry of the self-assembled monolayers (SAMs) of four butanethiols on Au(111) is described, the SAMs containing up to 12 individual C, S, or Au chiral centers per surface unit cell. This is facilitated by synthesis of enantiomerically pure 2-butanethiol (the smallest unsubstituted chiral alkanethiol), followed by in situ scanning tunneling microscopy (STM) imaging combined with density functional theory molecular dynamics STM image simulations. Even though butanethiol SAMs manifest strong headgroup interactions, steric interactions are shown to dominate SAM structure and chirality. Indeed, steric interactions are shown